phylogenomics | Topic | Ecosyste.ms: Repos

Topic: "phylogenomics"

merenlab/anvio

An analysis and visualization platform for 'omics data

Language: Python - Size: 745 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 470 - Forks: 148

Cibiv/IQ-TREE 📦

Efficient phylogenomic software by maximum likelihood

Language: C++ - Size: 65.4 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 180 - Forks: 45

tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

Language: Perl - Size: 11.3 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 139 - Forks: 38

CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: TypeScript - Size: 136 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 92 - Forks: 42

moshi4/ANIclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

Language: Python - Size: 184 MB - Last synced at: 3 days ago - Pushed at: 25 days ago - Stars: 80 - Forks: 10

JLSteenwyk/ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Language: Python - Size: 25.8 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 73 - Forks: 5

JLSteenwyk/PhyKIT

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

Language: Python - Size: 17.5 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 69 - Forks: 8

jamiemcg/BUSCO_phylogenomics

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Language: Python - Size: 347 KB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 64 - Forks: 9

vinuesa/get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Language: Perl - Size: 115 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 55 - Forks: 9

pblischak/HyDe

Hybridization detection using phylogenetic invariants

Language: Python - Size: 2.03 MB - Last synced at: 9 days ago - Pushed at: 7 months ago - Stars: 47 - Forks: 14

zhaotao1987/SynNet-Pipeline

Workflow for Building Microsynteny Networks

Language: Shell - Size: 3.78 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 47 - Forks: 27

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.

Language: Python - Size: 231 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 31 - Forks: 16

JLSteenwyk/orthofisher

a broadly applicable tool for automated gene identification and retrieval

Language: Python - Size: 81.9 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 31 - Forks: 1

almeidasilvaf/syntenet

An R package to infer and analyze synteny networks from protein sequences

Language: R - Size: 75.3 MB - Last synced at: 23 days ago - Pushed at: 5 months ago - Stars: 30 - Forks: 6

moshi4/CafePlotter

A tool for plotting CAFE5 gene family expansion/contraction result

Language: Python - Size: 3.77 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 29 - Forks: 3

hhandika/segul

An ultrafast and memory efficient tool for phylogenomics

Language: Rust - Size: 1.85 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 26 - Forks: 2

xflouris/libpll

Phylogenetic Likelihood Library

Language: C - Size: 3.06 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 26 - Forks: 7

edgardomortiz/Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Language: Python - Size: 77.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 25 - Forks: 6

reslp/phylociraptor

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Language: Python - Size: 3.36 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 25 - Forks: 6

JLSteenwyk/orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Language: Python - Size: 112 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 25 - Forks: 1

vinuesa/TIB-filoinfo

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

Language: Shell - Size: 160 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 22 - Forks: 5

GunzIvan28/rMAP

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

Language: Shell - Size: 6.27 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 22 - Forks: 17

zhangrengang/phytop

Visualing species tree from ASTRAL with gene tree discordance

Language: Python - Size: 1.81 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 20 - Forks: 4

dr-joe-wirth/phantasm

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

Language: Python - Size: 5.77 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 0

zhangrengang/SOI

Robust identification of orthologous Synteny with the Orthology Index

Language: Python - Size: 9.24 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 19 - Forks: 1

ChrisCreevey/clann

Clann: constructing consensus trees and supertrees from multiple source trees

Language: C - Size: 3.13 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 15 - Forks: 2

moshi4/FastDTLmapper 📦

Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method

Language: Python - Size: 38.9 MB - Last synced at: 10 days ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 4

quxiaojian/Bioinformatic_Scripts

common bioinformatic scripts

Language: Perl - Size: 5.47 MB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 15 - Forks: 17

abschneider/StrainHub

Welcome to the StrainHub Repo - Files and Data - StrainHub Online:

Language: HTML - Size: 10.8 MB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 4

merlyescalona/ngsphy

NGSphy: phylogenomic simulation of next-generation sequencing data

Language: Python - Size: 16.3 MB - Last synced at: 8 months ago - Pushed at: about 7 years ago - Stars: 14 - Forks: 6

damiendevienne/phylter

Detection of outlier genes and species in phylogenomics

Language: R - Size: 181 MB - Last synced at: 14 days ago - Pushed at: 3 months ago - Stars: 12 - Forks: 5

AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: HTML - Size: 68.5 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 12 - Forks: 42

jbpease/mvftools

Multisample Variant Format ToolKit

Size: 4.18 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 5

emilhaegglund/TADA

A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information

Language: Python - Size: 119 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 10 - Forks: 2

ekmolloy/njmerge

A tool for divide-and-conquer tree estimation via a shared distance matrix

Language: Python - Size: 4.77 MB - Last synced at: 4 months ago - Pushed at: about 6 years ago - Stars: 10 - Forks: 2

Rowena-h/BUSCOfilter

A tool to filter BUSCO output into single-copy gene files for phylogenomics

Language: Shell - Size: 45.9 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 9 - Forks: 1

rtfcoimbra/Coimbra-et-al-2021_CurrBiol

Code used to analyse WGS data of giraffe in Coimbra et al. 2021 (https://doi.org/10.1016/j.cub.2021.04.033)

Language: Shell - Size: 83 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 6

pblischak/hyde-cnn

Hybridization Detection with Convolutional Neural Networks

Language: Python - Size: 8.46 MB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 1

wrf/supermatrix

scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms

Language: Python - Size: 41.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 3

natapol/kitsune

a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.

Language: Python - Size: 7.33 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 2

BioJulia/Phylogenies.jl

The BioJulia package for working with phylogenetic trees and geneologies.

Language: Julia - Size: 446 KB - Last synced at: 8 days ago - Pushed at: almost 7 years ago - Stars: 8 - Forks: 4

baileyp1/PhylogenomicsPipelines

Two pipelines to perform phylogenomic analysis

Language: Pep8 - Size: 111 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 7 - Forks: 3

jlescroart/Lescroart2023 📦

Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)

Language: Python - Size: 623 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 0

peaselab/mvftools

Language: Python - Size: 846 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

atorresgalvis/TNT-scripts-for-phylogenomics

Scripts published in: Torres, A., Goloboff, P. A., & Catalano, S. A. (2022). Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology). Cladistics, 38(1), 103-125. doi:10. 1111/cla.12477

Size: 3.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 1

pythonLoader/QT-GILD

Official Implementation of QT-GILD

Language: Python - Size: 101 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

ekmolloy/fastmulrfs

Species tree estimation from multi-copy gene trees

Language: Python - Size: 389 KB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 1

tkchafin/FGTpartitioner

Parsimonious delimitation of large SNP datasets using the four gamete test

Language: Python - Size: 442 KB - Last synced at: 3 days ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 0

1KFG/Phylogenomics

Phylogenomics analyses for 1KFG project

Language: Shell - Size: 62.5 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 0

faylward/pangenomics

Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.

Language: Python - Size: 37.8 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 5

V-Z/sondovac

Sondovač is a script to create orthologous low-copy nuclear probes from transcriptome and genome skim data for target enrichment. For latest version check "releases".

Language: TeX - Size: 14.4 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 2

slipa17/Whole-genome-sequencing-and-comparative-genomics-of-human-lung-streptococcal-isolates

Genomic sequencing, phylogenetic analysis and comparative genomics by pan-genome analysis of human distal lung Streptococcus isolates.

Language: Shell - Size: 575 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 1

gi-bielefeld/sans

Alignment-free phylogenomic splits

Language: C++ - Size: 9.31 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 4 - Forks: 2

tomarovsky/BuscoClade

Snakemake pipeline to construct species phylogenies using BUSCOs

Language: Python - Size: 416 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 2

Rowena-h/GaeumannomycesGenomics

Scripts for Hill et al. (2025) doi:10.1186/s12864-025-11432-0 🌾

Language: R - Size: 3.83 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

V-Z/hybseq-scripts

Set of scripts to process HybSeq target enrichment HTS data (on computing grids).

Language: Shell - Size: 2.33 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 3

lonelyjoeparker/qmul-genome-convergence-pipeline

API and binaries for phylogenomic analyses, particularly comparison of input trees/alignments (CONTEXT) and detecting genomic convergence

Language: HTML - Size: 42.7 MB - Last synced at: 6 months ago - Pushed at: over 7 years ago - Stars: 4 - Forks: 2

chutter/AstralPlane

AstralPlane: R Package For Preparing, Running, Analyzing and Plotting from the Species Tree Program ASTRAL-III

Language: R - Size: 166 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 0

AKU-CITRIC-Center-for-Bioinformatics/ncov

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Size: 57.2 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

Rowena-h/FusariumLifestyles

Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085

Language: R - Size: 19.4 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3

jvanheld/SARS-CoV-2_origins

Analysis of insertions in the genomes and proteins of coronaviruses. Illustration: AvH. (2020). Covid-19 cracked <http://doi.org/10.5281/zenodo.3734643>

Language: HTML - Size: 345 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 7

jacksonhturner/orthogarden

ML phylogenetic inference for non-model organisms with short reads & assemblies

Language: Python - Size: 13.8 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 2 - Forks: 0

amarinderthind/CGRphylo

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

Language: R - Size: 1.12 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 2

XueyunF/nsp_phylogeo

Phylogenomics analysis of nine-spine stickleback

Language: Python - Size: 4.89 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

RhettRautsaw/PhyProbe

PhyProbe is a bioinformatic pipeline designed to extract phylogenetic loci from Next-Generation Sequencing datasets including RNAseq, WGS, and Sequence/Target Capture methodologies (e.g., AHE, UCEs).

Language: Python - Size: 890 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

ChrisCreevey/machete

Machete: Automated Likelihood decay indices and Maximum likelihood phlyogeny construction with PAUP*

Language: C - Size: 74.2 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

lepitaxa/lepitaxa.github.io

LEPITAXA – Lepidopteran Classification Project

Language: HTML - Size: 5.37 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

JBris/beast2-docker

Docker and Apptainer setup for the BEAST 2 software

Language: R - Size: 679 KB - Last synced at: 27 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

fomightez/simulated_data

A repository for code that generates various simulated data.

Language: Python - Size: 1.02 MB - Last synced at: 8 days ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

MafaldaSFerreira/Atlherr_inversion_evol

Evolutionary genomics of chromosomal inversions in Atlantic herring

Language: R - Size: 639 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

OlgaChern/Gentrius_2023SM

Data and Code for the manuscript "Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius"

Language: Shell - Size: 38.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

niconm89/BUSCO2Tree

This pipeline helps to build a phylogenetic tree using the BUSCO results over a group of species/genomes/proteomes/transcriptomes.

Language: Python - Size: 46.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

SethMusker/TargetVet

Target Capture (aka Hyb-seq) marker vetting using WGS data.

Language: R - Size: 83.9 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

mag-wolf/GEMOMA-to-Phylogeny

Building a fully automized pipeline for phylogenomic analyses based on the GEMOMA annotation pipeline

Language: Perl - Size: 53.8 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

meidanis-lab/rank-indel

Pipeline to build phylogenetic trees using the Rank distance

Language: Python - Size: 1.8 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Royal-Botanic-Gardens-Victoria/PAFTOL-taxonomy-classifier

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python scripts used below are also in your PATH #Download PAFTOL V2.0 Angio353 genes from Kew #After building the DB, the scripts kraken2paired.py and top_taxa.py can be used to identify taxonomy of unknown samples. #e.g. #kraken2paired.py "reads/*.fastq" kraken_results/ 0 24 kraken2_paftol2/ #top_taxa.py "kraken_results/*" kraken.out

Language: Python - Size: 11.7 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0