☆13Dec 4, 2025Updated 2 months ago
Alternatives and similar repositories for paPAML
Users that are interested in paPAML are comparing it to the libraries listed below
Sorting:
- HyPhy standalone analyses☆53Jan 5, 2026Updated last month
- This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager☆10Mar 19, 2024Updated last year
- An R package to perform systematic quality checks on comparative genomics analyses☆12Jan 12, 2024Updated 2 years ago
- Metabolic scanning and annotation of Metagenomes☆10Dec 18, 2025Updated 2 months ago
- Tutorial for using MCMCTree as implemented by Brown Lab at SIUC. For divergence time estimation on UCE datasets, for dendrobatid frogs.☆10Jun 19, 2020Updated 5 years ago
- distance based phylogenetic placement☆27Feb 28, 2024Updated 2 years ago
- PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding☆11Mar 31, 2021Updated 4 years ago
- package for interacting with the chromosome counts database (CCDB) at https://taux.evolseq.net/CCDB_web/☆13Jul 28, 2025Updated 7 months ago
- An integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing data☆14May 17, 2025Updated 9 months ago
- Parse scientific names using gnparser (https://github.com/gnames/gnparser)☆15Jan 1, 2026Updated 2 months ago
- Drawing 'dendrogram' using 'ggtree'☆13Nov 1, 2025Updated 4 months ago
- In this repo, I explain how can we use clusterProfiler and Tidyverse to perform (GO or KEGG) enrichment analysis in R.☆24Sep 20, 2023Updated 2 years ago
- Fast implementation of KofamScan optimized for high-memory systems using PyHMMER☆17Jan 13, 2026Updated last month
- Bayesian molecular clock dating tutorial with genome-scale datasets☆19Dec 4, 2021Updated 4 years ago
- 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
- Generate Galaxy tool descriptions automatically from QIIME 2 actions.☆20Jan 27, 2026Updated last month
- Plasmid analysis using rearrangement distances☆50Feb 19, 2026Updated last week
- A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models☆18Nov 29, 2022Updated 3 years ago
- 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
- EasyCodeML: A visual tool for analysis of selection using CodeML☆83May 7, 2023Updated 2 years ago
- R package for searching, downloading and analysis of EBI MGnify metagenomics data☆23Feb 13, 2026Updated 2 weeks ago
- Helper scripts for processing and visualization of phylogenetics datasets☆31Feb 19, 2024Updated 2 years ago
- phylobayes mpi☆28Feb 3, 2023Updated 3 years ago
- Ready-made Taxonomic Weights Repository☆26Mar 31, 2022Updated 3 years ago
- JTK -- a regional diploid genome assembler☆25Oct 20, 2024Updated last year
- Automatically exported from code.google.com/p/densitree☆29Jul 27, 2025Updated 7 months ago
- BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts☆72Nov 17, 2025Updated 3 months ago
- An R package with toolkits for tong's friends☆11Mar 18, 2025Updated 11 months ago
- ☆16Aug 17, 2023Updated 2 years ago
- paml documentation and tutorials☆68Jan 9, 2026Updated last month
- A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes☆30Apr 10, 2024Updated last year
- HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching☆36Aug 7, 2017Updated 8 years ago
- ☆33Jul 9, 2024Updated last year
- Convergent substitution detection tool based on the PCOC model☆31Dec 2, 2021Updated 4 years ago
- MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional ba…☆12Jul 11, 2025Updated 7 months ago
- HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high…☆10Apr 15, 2025Updated 10 months ago
- A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.☆28Feb 14, 2023Updated 3 years ago
- Automatic evaluation of HGTs☆30Jan 31, 2025Updated last year
- A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data☆30Apr 22, 2021Updated 4 years ago