CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.
☆23Nov 21, 2023Updated 2 years ago
Alternatives and similar repositories for caastools
Users that are interested in caastools are comparing it to the libraries listed below
Sorting:
- This is used to call Codeml to calculate the positive selection of gene in Branch-Sites Model.(Require codon sequence)☆18Nov 18, 2021Updated 4 years ago
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆45Nov 21, 2019Updated 6 years ago
- Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework☆24Nov 29, 2022Updated 3 years ago
- SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event.☆23Sep 23, 2024Updated last year
- Annotate Olfactory receptor CDS from genome☆10Apr 29, 2023Updated 2 years ago
- Segmental duplication detection tool☆16Feb 7, 2023Updated 3 years ago
- Strand and WGD aware syntenic gene identification☆15Oct 16, 2025Updated 4 months ago
- SYNPHONI is a tool designed for reconstructing the dynamic evolution of syntenic relationships across all scales of phylogenetic distance…☆12May 7, 2023Updated 2 years ago
- detectRuns: a R Package for Runs of Homozygosity and Runs of Heterozygosity☆12May 25, 2023Updated 2 years ago
- Convergent substitution detection tool based on the PCOC model☆31Dec 2, 2021Updated 4 years ago
- Newick tree processing☆13Feb 22, 2026Updated last week
- Calculate the dn/ds (also pn and ps) value of cds☆13Jul 11, 2020Updated 5 years ago
- This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager☆10Mar 19, 2024Updated last year
- Inferring natural selection by comparative population genomic analysis across species☆26Oct 31, 2023Updated 2 years ago
- Diamond2GO is a set of tools that can rapidly assign Gene Ontology (GO) terms and perform functional enrichment for large-scale functiona…☆26Feb 4, 2026Updated 3 weeks ago
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year
- From the comparison of two extant genomes and corresponding gene families, PhylDiag detects conserved segments, i.e. segments of chromoso…☆15Aug 7, 2023Updated 2 years ago
- ☆21Sep 12, 2019Updated 6 years ago
- De-novo Assembly Structural Variant Caller☆13Sep 15, 2016Updated 9 years ago
- Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence☆23Feb 9, 2026Updated 3 weeks ago
- ☆15Jul 21, 2022Updated 3 years ago
- ☆26Jan 26, 2026Updated last month
- Analysis of convergence between organismal traits and DNA/protein sequences☆63Jan 6, 2026Updated last month
- This python script can be used to detect Whole-genome duplication (WGD) with the dS based method.☆25Feb 22, 2019Updated 7 years ago
- Genome alignment and synteny plots☆33Jun 5, 2023Updated 2 years ago
- parallelLastz: Running Lastz in parallel☆17Sep 13, 2024Updated last year
- This is the standalone version of the EviAnn pipeline☆139Feb 5, 2026Updated 3 weeks ago
- ☆17Oct 21, 2024Updated last year
- HyPhy standalone analyses☆53Jan 5, 2026Updated last month
- ☆67Apr 9, 2024Updated last year
- ☆17Nov 9, 2020Updated 5 years ago
- BITACORA: A Bioinformatics tool for gene family annotation☆53Dec 10, 2025Updated 2 months ago
- Algorithm For Gene Order Reconstruction in Ancestors☆80Aug 16, 2025Updated 6 months ago
- The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).☆21Sep 9, 2021Updated 4 years ago
- A comprehensive pipeline for RNAseq data analysis☆22Aug 31, 2024Updated last year
- Gene Family Annotation Workflow☆11Mar 26, 2024Updated last year
- A genome-scale, fast, and precise segmental duplications mapping tool☆35Sep 11, 2024Updated last year
- Computational Analysis of Gene Expression Evolution☆45Aug 19, 2025Updated 6 months ago
- Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com…☆37Sep 30, 2024Updated last year