phylogenomics

There are 6 repositories under phylogenomics topic.

anvio
merenlab / anvio
An analysis and visualization platform for 'omics data
metagenomics metatranscriptomics pangenomics comparative-genomics science visualization bioinformatics phylogenomics population-genetics python javascript anvio
Language:Python 406
Cibiv / IQ-TREE
Efficient phylogenomic software by maximum likelihood
maximum-likelihood phylogenomics phylogenetics mixture-model iq-tree ultrafast-bootstrap model-selection
Language:C++ 181
tseemann / nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
bacteria report fastq denovo-assembly variant-calling genotyping resistome virulome phylogenomics public-health
Language:Perl 130
MicrobeTrace
CDCgov / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-visualization hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics genomics genomics-visualization genomic-data-analysis sequence-alignment
Language:TypeScript 83
ClipKIT
JLSteenwyk / ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics
Language:Python 54
PhyKIT
JLSteenwyk / PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python multiple-sequence-alignments
Language:Python 53
ANIclustermap
moshi4 / ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
python bioinformatics genomics phylogenetics phylogenomics visualization comparative-genomics taxonomy microbial-genomics
Language:Python 53
vinuesa / get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
phylogenomics population-genetics phylogenomics-pipeline species-trees markers genomics pipeline phylogenetics phylogenetic-trees codon-alignment maximum-likelihood orthologues species-delimitation microbiology core-genome perl r bash clock-hypothesis recombination
Language:Perl 47
zhaotao1987 / SynNet-Pipeline
Workflow for Building Microsynteny Networks
genome network-analysis phylogenomics synteny-network
Language:Shell 47
pblischak / HyDe
Hybridization detection using phylogenetic invariants
cython hybridization phylogenetic-networks phylogenomics python-package
Language:Python 39
jamiemcg / BUSCO_phylogenomics
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
bayesian bioinformatics evolution genomics maximum-likelihood phylogenetics phylogenomics
Language:Python 33
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.
bioinformatics phylogenomics
Language:Python 29
xflouris / libpll
Phylogenetic Likelihood Library
phylogenetics c likelihood phylogenomics
Language:C 26
orthofisher
JLSteenwyk / orthofisher
a broadly applicable tool for automated gene identification and retrieval
bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python
Language:Python 24
reslp / phylociraptor
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
bioinformatics genomics phylogenetics pipeline phylogenomics phylogenomics-pipeline snakemake species-tree maximum-likelihood
Language:Python 23
dr-joe-wirth / phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
bioinformatics phylogenomics taxonomy microbiology
Language:Python 20
moshi4 / CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result
bioinformatics molecular-evolution evolution phylogenetic-trees phylogenetics python matplotlib phylogenomics
Language:Python 20
orthosnap
JLSteenwyk / orthosnap
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python
Language:Python 19
almeidasilvaf / syntenet
An R package to infer and analyze synteny networks from protein sequences
comparative-genomics evolutionary-genomics network-science phylogenomics rstats synteny synteny-network
Language:R 18
rMAP
GunzIvan28 / rMAP
Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
bacteria eskape illumina mobilome phylogenomics resistome wgs
Language:Shell 18
vinuesa / TIB-filoinfo
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
bash-scripting bioinformatics-scripts blast linux-shell maximum-likelihood model-selection multiple-sequence-alignment phylogenetics reciprocal-blast-hits tutorials bioinformatics pangenomics phylogenomics
Language:Shell 17
abschneider / StrainHub
Welcome to the StrainHub Repo - Files and Data - StrainHub Online:
phylogenetics transmission-network phylogenomics phylogeography
Language:HTML 14
ChrisCreevey / clann
Clann: constructing consensus trees and supertrees from multiple source trees
supertrees algorithm bioinformatics constructing-consensus-trees species-trees phylogenomics
Language:C 14
merlyescalona / ngsphy
NGSphy: phylogenomic simulation of next-generation sequencing data
next-generation-sequencing phylogenomics read-counts gene-trees species-trees coverage targeted-sequencing
Language:Python 14
quxiaojian / Bioinformatic_Scripts
common bioinformatic scripts
extraction alignment matrix phylogenomics
Language:Perl 14
edgardomortiz / Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
alignment bioinformatics busco-lineages busco-orthologs genome-skimming high-throughput-sequencing hybridization-capture next-generation-sequencing ngs orthologs paralogs phylogenetics phylogenomics phylotranscriptomics rna-seq target-capture whole-genome-sequencing
Language:Python 13
hhandika / segul
An ultrafast and memory efficient tool for phylogenomics
rust command-line-tool bioinformatics phylogenetics phylogenomics alignment
Language:Rust 13
moshi4 / FastDTLmapper
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
python bioinformatics dtl-reconciliation phylogenomics phylogenetics functional-analysis genomics pipeline comparative-genomics molecular-evolution gene-ontology
Language:Python 12
jbpease / mvftools
Multisample Variant Format ToolKit
molecular-evolution population-genomics population-genetics phylogenetics phylogenomics genomics
11
rtfcoimbra / Coimbra-et-al-2021_CurrBiol
Code used to analyse WGS data of giraffe in Coimbra et al. 2021
bioinformatics genomics phylogenomics population-genomics speciation giraffe
Language:Shell 10
AABoyles / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-analysis network-graph network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment
Language:HTML 9
ekmolloy / njmerge
A tool for divide-and-conquer tree estimation via a shared distance matrix
divide-and-conquer phylogenetics phylogenomics gene-trees species-trees
Language:Python 9
natapol / kitsune
a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.
kitsune kmer-length bioinformatics phylogenomics
Language:Python 9
pblischak / hyde-cnn
Hybridization Detection with Convolutional Neural Networks
convolutional-neural-networks deep-learning hybridization phylogenomics python3
Language:Python 9
emilhaegglund / TADA
A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information
bioinformatics-pipeline phylogenomics
Language:Python 8
FusariumLifestyles
Rowena-h / FusariumLifestyles
Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣
bioinformatics comparative-genomics fungi genome-annotation genome-assembly phylogenomics
Language:R 8