phylogenomics
There are 124 repositories under phylogenomics topic.
merenlab/anvio
An analysis and visualization platform for 'omics data
Cibiv/IQ-TREE
Efficient phylogenomic software by maximum likelihood
tseemann/nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
CDCgov/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
moshi4/ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
JLSteenwyk/ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
JLSteenwyk/PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
jamiemcg/BUSCO_phylogenomics
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
vinuesa/get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
zhaotao1987/SynNet-Pipeline
Workflow for Building Microsynteny Networks
pblischak/HyDe
Hybridization detection using phylogenetic invariants
TheBrownLab/PhyloFisher
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.
JLSteenwyk/orthofisher
a broadly applicable tool for automated gene identification and retrieval
xflouris/libpll
Phylogenetic Likelihood Library
almeidasilvaf/syntenet
An R package to infer and analyze synteny networks from protein sequences
moshi4/CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result
JLSteenwyk/orthosnap
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
dr-joe-wirth/phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
edgardomortiz/Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
GunzIvan28/rMAP
Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
hhandika/segul
An ultrafast and memory efficient tool for phylogenomics
reslp/phylociraptor
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
vinuesa/TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
zhangrengang/phytop
Visualing species tree from ASTRAL with gene tree discordance
abschneider/StrainHub
Welcome to the StrainHub Repo - Files and Data - StrainHub Online:
quxiaojian/Bioinformatic_Scripts
common bioinformatic scripts
ChrisCreevey/clann
Clann: constructing consensus trees and supertrees from multiple source trees
moshi4/FastDTLmapper
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
merlyescalona/ngsphy
NGSphy: phylogenomic simulation of next-generation sequencing data
zhangrengang/SOI
Robust identification of orthologous Synteny with the Orthology Index
AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Rowena-h/BUSCOfilter
A tool to filter BUSCO output into single-copy gene files for phylogenomics
Rowena-h/FusariumLifestyles
Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣
rtfcoimbra/Coimbra-et-al-2021_CurrBiol
Code used to analyse WGS data of giraffe in Coimbra et al. 2021
emilhaegglund/TADA
A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information
natapol/kitsune
a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.