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phylogenetics

Here are 373 public repositories matching this topic...

biopython / biopython

Open

Define SeqFeature sub for integer offset

peterjc commented Jan 1, 2022

See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and __add__, need to do the same specifically for integer offsets.

Workaround feature + (-5) instead of feature - 5, see https://twitter.com/tomeraltman/status/1473764959347638273

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Enhancement good first issue

Open

silence warnings PDBConstructionWarning in test_PDB_StructureAlignment.py

4

Open

PAML run method docstrings - return value

16

Find more good first issues

etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

visualization python phylogenetics tree-structure phylogenomic treeview

Updated Feb 4, 2022
Python

amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

bioinformatics mpi phylogenetics pthreads maximum-likelihood

Updated Jan 31, 2022
C++

GTDBTk

Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

nomenclature taxonomy phylogenetics bacteria archaea species-assignments

Updated Dec 9, 2021
Python

CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees

java evolution beast phylogenetics bayesian-inference mcmc

Updated Jan 30, 2022
Java

NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

bioinformatics phylogenetics research-tool bayesian-inference markov-chain-monte-carlo

Updated Nov 18, 2021
C

edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

snps binary nexus vcf phylogenetics alignment fasta snapp phylip vcf-files polyploid haploid phylogenetic-analysis outgroup convert-snps vcf-format phylip-matrix diploid

Updated Nov 19, 2021
Python

veg / hyphy

HyPhy: Hypothesis testing using Phylogenies

science c-plus-plus phylogenetics bioinfomatics

Updated Feb 2, 2022
HyPhy

Cibiv / IQ-TREE

Efficient phylogenomic software by maximum likelihood

phylogenetics model-selection mixture-model maximum-likelihood phylogenomics iq-tree ultrafast-bootstrap

Updated Nov 4, 2021
C++

beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

java evolution beast phylogenetics mcmc bayesian-analysis

Updated Jan 27, 2022
Java

stephaneguindon / phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

evolution phylogenetics mcmc

Updated Feb 1, 2022
C

neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Updated Feb 4, 2022
Python

biologyguy / BuddySuite

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

python workflow bioinformatics command-line biology dna protein phylogenetics alignment

Updated Dec 6, 2021
Python

FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers

simulation phylogenetics molecular-evolution

Updated Nov 29, 2021
C++

tskit

tskit-dev / tskit

Open

add watterson's theta

1

mufernando commented Jun 23, 2021

this would be simple, as watterson's theta is

ts.segregating_sites()/sum([1/i for i in range(1, ts.num_samples])

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enhancement good first issue statistics

Open

Add contig_id to tskit vcf CLI

Open

Support negative indexing in Tree.unrank

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hahnlab / CAFE

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

bioinformatics phylogenetics gene-families

Updated Apr 7, 2021
C++

ODiogoSilva / TriFusion

Streamlining phylogenomic data gathering, processing and visualization

visualization python gui genetics kivy phylogenetics orthologues phylogenomic

Updated Sep 26, 2018
Python

usher

yatisht / usher

Ultrafast Sample Placement on Existing Trees

phylogenetics genome-browser phylogenetic-placement maximum-parsimony usher sars-cov-2

Updated Feb 4, 2022
C++

evogytis / baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

visualisation phylogenetics

Updated Jan 25, 2022
Python

Zsailer / phylopandas

Pandas DataFrames for phylogenetics

python pandas biopython phylogenetics

Updated Jun 6, 2021
Python

MicrobeTrace

CDCgov / MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics genomics phylogenetic-trees phylogenetics epidemiology network-visualization hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens

Updated Jan 27, 2022
TypeScript

hahnlab / CAFE5

Version 5 of the CAFE phylogenetics software

bioinformatics phylogenetics gene-family

Updated Jan 14, 2022
C++

r2g

yangwu91 / r2g

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

bioinformatics bioinformatics-pipeline phylogenetics orthology homology ncbi-sra gene-sequence-retrieval

Updated Apr 2, 2021
Python

Pbdas / epa-ng

Massively parallel phylogenetic placement of genetic sequences

bioinformatics openmp mpi phylogenetics placement taxonomic-classification mpi-io

Updated Dec 8, 2021
C++

lczech / genesis

A library for working with phylogenetic and population genetic data.

c-plus-plus phylogenetic-trees phylogenetics population-genetics evolutionary-placement phylogenetic-data placement pool-sequencing phylogenetic-placements

Updated Jan 28, 2022
C++

lczech / gappa

A toolkit for analyzing and visualizing phylogenetic (placement) data

c-plus-plus phylogenetics genesis evolutionary-placement phylogenetic-data placement phylogenetic-placement gappa

Updated Jan 17, 2022
C++

vinuesa / get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics, population genetics and genomic taxonomy

bash r pipeline genomics perl phylogenetic-trees phylogenetics markers orthologues microbiology population-genetics codon-alignment maximum-likelihood phylogenomics species-trees recombination core-genome species-delimitation phylogenomics-pipeline clock-hypothesis

Updated Oct 12, 2021
Perl

cmzmasek / forester

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research

visualization ruby java genomics biology evolution computational-biology phylogenetic-trees phylogenetics

Updated Sep 30, 2021
Java

niemasd / FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

docker modular virus simulation evolution transmission phylogenetics robust hiv evolution-simulator transmission-network

Updated Jan 24, 2022
Python

tgvaughan / icytree

Browser-based utility for phylogenetic tree visualisation.

visualization phylogenetics

Updated Jan 30, 2022
JavaScript

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