orthology-inference

There are 1 repository under orthology-inference topic.

drostlab / orthologr
Genome wide orthology inference and dNdS estimation
blast-searches orthology-inference comparative-genomics-studies genomics sequence-alignments blast comparative dnds-estimation codon-alignment r entire-genomes orthologous-genes biomartr species comparing-genomes genomics-studies retrieve-genomes comparative-genomics proteome sequence-alignment
Language:R 84
DRL / kinfin
Taxon-aware analysis of clustered protein sequences
bioinformatics proteome-clustering orthology-inference blaxterlab comparative-genomics
Language:Python 29
datasnakes / OrthoEvolution
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
python bioinformatics orthologs biology phylogenetics ncbi ftp blast qsub orthology-inference pbs bash shell genetics sequence-alignment orthology orthologues sge biosql data-science
Language:Python 27
Rinoahu / SwiftOrtho
A high performance tool to identify orthologs and paralogs across genomes.
orthologs protein-sequences orthology-relationships paralogs cluster genome orthology-inference
Language:Python 26
univieCUBE / deepnog
Protein orthologous group assignment with deep learning
protein-sequences orthology-inference orthology-assignments deep-learning machine-learning
Language:Python 25
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
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
PhyloSofS-Team / thoraxe
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
bioinformatics alternative-splicing protein-evolution exon homology orthology-inference
Language:Python 10
glarue / reciprologs
Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.
orthologs orthology-inference bioinformatics homology
Language:Python 9
BIONF / fDOG
Feature-aware Directed OrtholoG search
orthologs orthology-inference orthology python
Language:Python 8
BIONF / HaMStR
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
homology homology-search orthology-inference orthology
Language:Perl 8
wrf / supermatrix
scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms
supermatrix supermatrix-alignment phylogenetics phylogenomics orthologs orthology-inference rshiny quality-control
Language:Python 8
arendsee / synder
Trace intervals between genomes using a synteny map
synteny bioinformatics orthology-inference interval-tree
Language:C++ 7
rbhXpress
SamiLhll / rbhXpress
A shell script that uses diamond to compute the reciprocal best hits between two proteomes in a rush.
bioinformatics-scripts orthology-inference
Language:Shell 4
fethalen / phylopypruner
Tree-based orthology inference with functionality for reducing contamination
bioinformatics phylogenetics orthology-inference orthology orthology-assignments
Language:Python 3
datasnakes / orthoevol-snakemake
A snakemake workflow for the OrthoEvol python package.
orthoevol orthology-inference snakemake snakemake-pipelines snakemake-workflow
Language:Python 1
fethalen / orthoquoll
A stand-alone tool for evaluating simple statistics of orthologs
phylogenetics phylogenetic-tree orthology-inference orthology-assignments orthology-relationships orthology
Language:Python 1
UdeS-CoBIUS / TranscriptOrthology
Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach
algorithm alternative-splicing clustering evolution isoorthology orthology-inference computational-biology
Language:Python 1
alepfu / vog-eda
EDA of virus orthologous groups (VOGs) from VOGDB and eggNOG
orthology-inference viral-genomics eda
Language:Jupyter Notebook 0
BIONF / dcc2
Dynamic core orthologs compilation tool
orthology orthology-inference oma hamstr h1s python
Language:Python 0
CyanoWorld / reciprocal_blast_pipeline
Reciprocal BLAST analysis pipeline with Snakemake and Django
blast snakemake django biopython docker orthology-inference
Language:HTML