GET_PHYLOMARKERS_v1.2.10_09042019

Updated paup binaries (va165) for Linux (Ubuntu) and MacOS X

GET_PHYLOMARKERS_v1.2.9_02012019

• updates IQ-Tree to v. 1.6.9

GET_PHYLOMARKERS_v1.2.8_18112018

• updates PAUP* to build 164 (Linux and MacOSX)
• updates IQ-Tree to v. 1.6.8
• added new function print_software_versions() to run_get_phylomarkers_pipeline.sh v.2.2.7_14Nov2018
• added more input file name cleanup code to remove characters like ',/;()[]: from input files that may interfere with the shell; run_get_phylomarkers_pipeline.sh 2.2.6_3Oct2018

GET_PHYLOMARKERS_v1.2.7_11072018

• Contains updated linux and macosx binaries for iqtree and paup
• improved documentation
• some minor bug fixes

GET_PHYLOMARKERS_v1.2.6_04042018

• Paper accepted in Front. Microbiol. | doi: 10.3389/fmicb.2018.00771
• Includes link to prepint @bioRxiv
• Minor fixes to messages printed to screen

GET_PHYLOMARKERS_v1.2.5_31032018

GET_PHYLOMARKERS_v1.2.5_31032018 provides the following fixes and improvements:

• updated IQ-TREE to v1.6.3
• updated paup*4a to release 161
• improved installation instructions and online tutorial
• system-wide installation provided for users with root privileges
• minor bug fixes

GET_PHYLOMARKERS_v1.2.4_08022018

GET_PHYLOMARKERS_v1.2.4_08022018 contains fixes to:

• the set_pipeline_environment function in run_get_phylomarkers_pipeline.sh and estimate_pangenome_phylogenies.sh, which should now work correctly on macos x machines.
• The set_pipeline_environment function was activated in estimate_pangenome_phylogenies.sh so that it can find the proper binaries and auxiliary scripts.

GET_PHYLOMARKERS_v1.2.3_07022018

GET_PHYLOMARKERS

Changes in this release

• This is release v1.2.3 of GET_PHYLOMARKERS (Feb. 7th, 2018). Includes a statically compiled and stripped bc binary. -C flag prints the codon tables. Extended manual y tutorial.

GET_PHYLOMARKERS_v1.2.2_04022018

GET_PHYLOMARKERS

Changes in this release

• This is release v1.2.2 of GET_PHYLOMARKERS (Feb. 4th, 2018). Minor fix in cleanup/tidying of directories in run_get_phylomarkers_pipeline.sh v2.1.2_4Feb18. -v flag prints list of system dependencies, like GET_HOMOLOGUES.
• Detailed instructions were added to INSTALL.md explaining how to setup the Docker environment on a host machine.
• The tutorial was significantly expanded to include detailed instruction on how to share directories on the host machine with a Docker container. This is illustrated with the test_sequences/ directory that ships with GET_PHYLOMARKERS.
• This release matches the Docker image tagged version 01022018-2.1.2_4Feb18.

General description

• It's a software package designed to identify optimal orthologous clusters to infer genome phylogenies at the DNA or protein levels. It can also select highly informative neutral markers for population genetics.
• It implements a pipeline to filter orthologous gene clusters computed by GET_HOMOLOGUES to exclude those with evidence for recombination or producing "outlier" and poorly resolved gene trees.
• The top-scoring markers are concatenated into a supermatrix, which is used to estimate species trees under the maximum-likelihood (ML) criterion, using state-of-the-art fast ML tree searching algorithms (FastTree and IQ-TREE).
• GET_PHYLOMARKERS can also estimate ML and parsimony trees from the pan-genome matrix, including unsupervised learning methods to detect optimal clusters of genomes from pan-genome and average genomic distance matrices.
• It has a detailed manual and a tutorial demonstrating how to run the full pipeline using a toy data set.
• We highly recommend that you download the Docker image, which bundles GET_PHYLOMARKERS with GET_HOMOLOGUES, ready to use on any platform. This is the easiest way to get the full pipeline up and running, avoiding potential architecture-specific configuration and installation problems of the second-party dependencies (Perl modules, R packages, binaries ...) required by these software suites.