SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system
MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
THE DARLING LAB
Compiling mauveAligner from source on Linux. Although Mauve is provided as a pre-compiled binary for Windows, Linux, and Mac OS X, we also make the source code available so that users can modify Mauve and compile it on other platforms. SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
THE DARLING LAB
Compiling mauveAligner from source on Linux. Although Mauve is provided as a pre-compiled binary for Windows, Linux, and Mac OS X, we also make the source code available so that users can modify Mauve and compile it on other platforms. THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
OPENINGS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
Compiling mauveAligner from source on Linux. Although Mauve is provided as a pre-compiled binary for Windows, Linux, and Mac OS X, we also make the source code available so that users can modify Mauve and compile it on other platforms. INITIAL SETUP
Go to launch.genome.edu.au. In "advanced options"->Flavor, select "GVL 4.2.0 Beta". Click "Create a cluster". Be patient (coffee might help), when the cluster has fully booted click the web console link. Occasionally the GVL web launcher fails to recognize that your GVL instance has completed launching. When this happens the GVL web console can
THE DARLING LAB
Developing the Mauve GUI in Eclipse. The Mauve graphical user interface (GUI) is a Java program that provides a front-end for constructing alignments with the command-line mauveAligner program in addition to offering interactive browsing of the alignment results. NOT SO FAST, FASTTREE Not so fast, FastTree. Mar 23, 2015. important: see update at bottom of page Recently, much of the microbiology world has been sucked into a vortex called genomic epidemiology. This is not entirely a bad thing. Genomic data can be orders of magnitude more informative than MLST data when it comes to inferring the ancestry of an isolated microbe.
INDEX OF /MAUVE/SNAPSHOTS/2015/2015-02-26/WINDOWS Index of /mauve/snapshots/2015/2015-02-26/windows. Name Last modified Size Description : Parent Directory - Microsoft.VC80.OpenMP/ 2015-02-26 21:10
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from INITIAL SETUP
Go to launch.genome.edu.au. In "advanced options"->Flavor, select "GVL 4.2.0 Beta". Click "Create a cluster". Be patient (coffee might help), when the cluster has fully booted click the web console link. Occasionally the GVL web launcher fails to recognize that your GVL instance has completed launching. When this happens the GVL web console can
THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
Compiling mauveAligner from source on Linux. Although Mauve is provided as a pre-compiled binary for Windows, Linux, and Mac OS X, we also make the source code available so that users can modify Mauve and compile it on other platforms. FILEZILLA SECURE FTP Add a "New Site". Copy and paste the NeCTAR instance IP address into the Host box. Set the protocol to SFTP. Select "Interactive" logon type. For GVL, the default user is "root". Unfortunately, this can vary with image. Hit "Connect". In the small message log window, you should see FileZilla and your running instance communicating. THE DARLING LAB
Developing the Mauve GUI in Eclipse. The Mauve graphical user interface (GUI) is a Java program that provides a front-end for constructing alignments with the command-line mauveAligner program in addition to offering interactive browsing of the alignment results. SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from INITIAL SETUP
Go to launch.genome.edu.au. In "advanced options"->Flavor, select "GVL 4.2.0 Beta". Click "Create a cluster". Be patient (coffee might help), when the cluster has fully booted click the web console link. Occasionally the GVL web launcher fails to recognize that your GVL instance has completed launching. When this happens the GVL web console can
THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
Compiling mauveAligner from source on Linux. Although Mauve is provided as a pre-compiled binary for Windows, Linux, and Mac OS X, we also make the source code available so that users can modify Mauve and compile it on other platforms. FILEZILLA SECURE FTP Add a "New Site". Copy and paste the NeCTAR instance IP address into the Host box. Set the protocol to SFTP. Select "Interactive" logon type. For GVL, the default user is "root". Unfortunately, this can vary with image. Hit "Connect". In the small message log window, you should see FileZilla and your running instance communicating. THE DARLING LAB
Developing the Mauve GUI in Eclipse. The Mauve graphical user interface (GUI) is a Java program that provides a front-end for constructing alignments with the command-line mauveAligner program in addition to offering interactive browsing of the alignment results. SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system OPENINGS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
REVIEWS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the INITIAL SETUP
Go to launch.genome.edu.au. In "advanced options"->Flavor, select "GVL 4.2.0 Beta". Click "Create a cluster". Be patient (coffee might help), when the cluster has fully booted click the web console link. Occasionally the GVL web launcher fails to recognize that your GVL instance has completed launching. When this happens the GVL web console can
NOT SO FAST, FASTTREE Not so fast, FastTree. Mar 23, 2015. important: see update at bottom of page Recently, much of the microbiology world has been sucked into a vortex called genomic epidemiology. This is not entirely a bad thing. Genomic data can be orders of magnitude more informative than MLST data when it comes to inferring the ancestry of an isolated microbe.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system OPENINGS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
REVIEWS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the INITIAL SETUP
Go to launch.genome.edu.au. In "advanced options"->Flavor, select "GVL 4.2.0 Beta". Click "Create a cluster". Be patient (coffee might help), when the cluster has fully booted click the web console link. Occasionally the GVL web launcher fails to recognize that your GVL instance has completed launching. When this happens the GVL web console can
NOT SO FAST, FASTTREE Not so fast, FastTree. Mar 23, 2015. important: see update at bottom of page Recently, much of the microbiology world has been sucked into a vortex called genomic epidemiology. This is not entirely a bad thing. Genomic data can be orders of magnitude more informative than MLST data when it comes to inferring the ancestry of an isolated microbe.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system MAUVE - DARLING LAB
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
PEOPLE - DARLING LAB People. Our group during a coastal research retreat in February 2019. Current members. Aaron Darling – Group Leader University of Technology Sydney, Building 4, Level 7 email: aaron.darling (at) uts.edu.autwitter: @koadman | google scholar | UTS staff profile Daniela Gaio – Ph.D. student, metagenomics of probiotic and antibiotic treatments in a model system OPENINGS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
REVIEWS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the INITIAL SETUP
Go to launch.genome.edu.au. In "advanced options"->Flavor, select "GVL 4.2.0 Beta". Click "Create a cluster". Be patient (coffee might help), when the cluster has fully booted click the web console link. Occasionally the GVL web launcher fails to recognize that your GVL instance has completed launching. When this happens the GVL web console can
NOT SO FAST, FASTTREE Not so fast, FastTree. Mar 23, 2015. important: see update at bottom of page Recently, much of the microbiology world has been sucked into a vortex called genomic epidemiology. This is not entirely a bad thing. Genomic data can be orders of magnitude more informative than MLST data when it comes to inferring the ancestry of an isolated microbe.
SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. MAUVE - DARLING LABDOWNLOAD MAUVEPEOPLEINTRODUCTIONBENCHMARKINGVERSION HISTORYMAUVEALIGNER
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Annotate an assembled genome with Prokka. This tutorial assumes you have already assembled a genome with SPAdes inside the Microbial GVL. See the "Genome assembly with SPAdes" page for instructions on how to do that.Launch the Prokka annotation THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the THE DARLING LAB
Developing the Mauve GUI in Eclipse. The Mauve graphical user interface (GUI) is a Java program that provides a front-end for constructing alignments with the command-line mauveAligner program in addition to offering interactive browsing of the alignment results. SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. MAUVE - DARLING LABDOWNLOAD MAUVEPEOPLEINTRODUCTIONBENCHMARKINGVERSION HISTORYMAUVEALIGNER
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
THE DARLING LAB
Mauve release archive. An archive of earlier Mauve releases for all platforms is available. Documentation. We provide a Mauve User’s Guide containing detailed information on how to operate the Mauve software.. Support. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make THE DARLING LAB
An introduction to Mauve. Over the course of evolution, genomes can undergo many small and large-scale changes. Local changes such as nucleotide substitution and indels have been observed in comparative studies of individual genes. THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
The display layout. The alignment display is organized into one horizontal “panel” per input genome sequence. Each genome’s panel contains the name of the genome sequence, a scale showing the sequence coordinates for that genome, and a single black horizontal center line.
THE DARLING LAB
When a genome alignment is created, Mauve creates several output files containing data related to the alignment. Two of these files, the .mauve and .alignment files actually contain the alignment in two different formats.
GENOME ANNOTATION WITH PROKKA Click the "NGS: Annotation" link at left. Scroll down and select "Prokka" in the left side drop down menu. Set the "Locus tag prefix" to a single letter, e.g. N. Select "Yes" for "Force GenBank/ENA/DDJB compliance (--compliant)". This is essential in order to visualize annotations in the Mauve software. Set the sequencing centre name to a THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the THE DARLING LAB
Developing the Mauve GUI in Eclipse. The Mauve graphical user interface (GUI) is a Java program that provides a front-end for constructing alignments with the command-line mauveAligner program in addition to offering interactive browsing of the alignment results. SOFTWARE - DARLING LAB Software Current software projects. Our group is currently involved in the following software development projects. PhyloSift - phylogenetic analysis of genomes and metagenomes PhyloSift is a re-implementation and extension of the original amphora approach to reconstructing metagenome phylogeny and taxonomy. PROJECTS - DARLING LAB Projects. Our group has several ongoing research projects that roughly fall into the following themes. Algorithms for metagenome analysis. Our work in this space includes the development of new analysis methods as well as contributing to community-driven efforts to evaluate the performance of publicly available metagenome data analysis methods.
OPENINGS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
REVIEWS - DARLING LAB The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
THE DARLING LAB
When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics.The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the THE DARLING LAB
Compiling mauveAligner from source on Linux. Although Mauve is provided as a pre-compiled binary for Windows, Linux, and Mac OS X, we also make the source code available so that users can modify Mauve and compile it on other platforms. PATTERNS OF GENOME REARRANGEMENT IN BACTERIAL POPULATIONS software. The methods for genome rearrangement analysis have been implemented in a set of scripts and programs collectively referred to as barphlye. barphlye makes use of the BADGER 1.01b software for MCMC analysis of inversion phylogeny, written by Donald Simon and Bret Larget. The latest release of barphlye may be downloaded here.. A full barphlye analysis also depends on R, available from THE DARLING LAB
Developing the Mauve GUI in Eclipse. The Mauve graphical user interface (GUI) is a Java program that provides a front-end for constructing alignments with the command-line mauveAligner program in addition to offering interactive browsing of the alignment results. INITIAL SETUP
Starting up the Genomics Virtual Lab A quick video tutorial. These tutorials use the Genomics Virtual Lab inside the NeCTAR research cloud. This is an Australian the Darling lab | computational (meta)genomics Blog Mauve Openings People Projects Publications Reviews Software Tutorials
* the Darling lab | computational (meta)genomics * aaron.darling@uts.edu.au * koadman
* koadman
The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.
