This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.
☆38Jan 3, 2026Updated 4 months ago
Alternatives and similar repositories for MACSE_V2_PIPELINES
Users that are interested in MACSE_V2_PIPELINES are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- babette is an R package to work with BEAST2☆46Mar 13, 2026Updated last month
- ☆19Dec 5, 2020Updated 5 years ago
- ☆26Apr 14, 2021Updated 5 years ago
- ☆10Mar 24, 2025Updated last year
- A massively parallel tool for model selection and tree inference on thousands of genes☆51Mar 4, 2024Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Alignment-Based Sequence extraction☆15Feb 14, 2022Updated 4 years ago
- Posterior summarisation in Bayesian phylogenetics☆70Sep 27, 2025Updated 7 months ago
- VESPA: Very large-scale Evolutionary and Selective Pressure Analyses☆15Mar 18, 2022Updated 4 years ago
- Lightweight python library for predicting the difficulty of alignments in phylogenetics☆23Dec 6, 2025Updated 4 months ago
- ☆16Apr 11, 2026Updated 3 weeks ago
- FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignmen…☆35Jun 12, 2024Updated last year
- Code for computing various support scores for internodes☆19Apr 7, 2020Updated 6 years ago
- ☆35Dec 24, 2020Updated 5 years ago
- R package to run BEAST2☆11Dec 8, 2025Updated 4 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆241Updated this week
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆30Feb 23, 2026Updated 2 months ago
- R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)☆17Mar 22, 2026Updated last month
- ☆46Sep 5, 2023Updated 2 years ago
- Materials for the INF 515: Comparative Genomics course at NAU taught by Prof. Marc Tollis☆13Apr 3, 2025Updated last year
- paml documentation and tutorials☆70Jan 9, 2026Updated 3 months ago
- Accurate Species TRee ALgorithm☆277Apr 1, 2024Updated 2 years ago
- Welcome to Physcraper’s repository! Automatic gene tree updating using the Open Tree of Life.☆13May 13, 2022Updated 3 years ago
- ☆11Dec 12, 2024Updated last year
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- A Nextflow pipeline for running synteny analysis.☆16Apr 24, 2026Updated last week
- ☆13Apr 22, 2026Updated last week
- An R package to perform systematic quality checks on comparative genomics analyses☆12Mar 5, 2026Updated last month
- ☆12Mar 11, 2025Updated last year
- An R package to infer and analyze synteny networks from protein sequences☆38Jul 23, 2025Updated 9 months ago
- Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.☆12Feb 27, 2019Updated 7 years ago
- ContScout sequence contamination filter tool☆26Dec 28, 2025Updated 4 months ago
- Workflow to detect and phase hybrids in target capture data☆20Mar 9, 2023Updated 3 years ago
- PHYLOgenomic analysis pipeline for HERBarium specimens☆17Feb 9, 2026Updated 2 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2☆13Dec 8, 2025Updated 4 months ago
- a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.☆15Nov 21, 2024Updated last year
- Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction☆11Sep 29, 2014Updated 11 years ago
- ☆36Mar 5, 2026Updated last month
- K-mer based classifier for Y-contig identification from Whole Genome Assemblies☆13Feb 19, 2020Updated 6 years ago
- Bayesian molecular clock dating tutorial with genome-scale datasets☆19Dec 4, 2021Updated 4 years ago
- ☆22Mar 25, 2014Updated 12 years ago