{"repo":"vinuesa/get_phylomarkers","free":true,"listed":false,"github":"https://github.com/vinuesa/get_phylomarkers","clone":"git clone https://github.com/vinuesa/get_phylomarkers.git","description":"A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches","language":"Perl","stars":60,"topics":["phylogenomics","population-genetics","phylogenomics-pipeline","species-trees","markers","genomics","pipeline","phylogenetics","phylogenetic-trees","codon-alignment"],"license":null,"category":"machine-learning","readme_excerpt":"GET PHYLOMARKERS GET PHYLOMARKERS (Vinuesa et al., 2018) is an open-source software package for selecting optimal markers for microbial phylogenomics and species tree estimation . It implements a bioinformatics pipeline to filter core-genome gene clusters computed by the companion package GET HOMOLOGUES , and selects only those with optimal attributes for phylogenetic inference using maximum likelihood (ML). The multiple sequence alignments of the filtered loci are concatenated into a supermatrix to estimate a species tree using the state-of-the-art fast ML tree searching algorithms FastTree or IQ-TREE. It also estimates ML and parsimony trees from the pan-genome matrix, including unsupervised learning methods. We have also tested it successfully with plant coding sequences (details here). GET PHYLOMARKERS 2 Starting with release 2.0.0 (2022-11-20), GET PHYLOMARKERS also computes a concatenation-independent species tree from the ML gene trees estimated from top-scoring alignments using ASTRAL-III . Release 2.1.0 (2024-03-31) introduced maximal matched-pairs tests to assess violations of the data to the Stationarity, Reversibility, and Homogeneity ( SRH ) assumptions made by maximum-likelihood phylogenetic models, as implemented in IQ-TREE. Additionally, ASTRAL-IV is used to estimate the species tree directly from the filtered ML source gene trees, which computes terminal and internal branch lengths in substitution-per-site units. Release 2.2.0 (v2.2.0, 2024-04-14) introduced ","default_branch":null,"files":null,"tree":[],"storefront":"/r/vinuesa","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/vinuesa/get_phylomarkers/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}