STAG: Species Tree from All Genes
☆35Dec 10, 2018Updated 7 years ago
Alternatives and similar repositories for STAG
Users that are interested in STAG are comparing it to the libraries listed below
Sorting:
- STRIDE: Species Tree Root Inference from Gene Duplication Events☆11Aug 28, 2018Updated 7 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
- 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
- The final version 2 release of our software to detect core genes in eukaryotic genomes☆29Mar 31, 2015Updated 10 years ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated 10 months ago
- Fast, accurate species tree estimation.☆12Aug 29, 2024Updated last year
- Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve o…☆11Jun 19, 2025Updated 8 months ago
- Implementation of the TreeShrink problem☆54Sep 13, 2024Updated last year
- use paired-end transcriptome reads to scaffold genomes☆11May 30, 2019Updated 6 years ago
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 7 years ago
- Version 5 of the CAFE phylogenetics software☆161Feb 12, 2025Updated last year
- Analyzing combinations of codon substitution histories☆46Updated this week
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆57Jan 26, 2023Updated 3 years ago
- Extensive de-novo TE Annotator☆430Oct 12, 2025Updated 4 months ago
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.☆18Apr 24, 2024Updated last year
- SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity …☆93Nov 24, 2025Updated 3 months ago
- Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees/networks)☆20Feb 23, 2026Updated last week
- Accurate Species TRee ALgorithm☆273Apr 1, 2024Updated last year
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated 11 months ago
- Clann: constructing consensus trees and supertrees from multiple source trees☆18Mar 23, 2025Updated 11 months ago
- Fast and frugal disk based k-mer counter☆14Apr 1, 2021Updated 4 years ago
- ☆24Dec 15, 2025Updated 2 months ago
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆226Jan 4, 2026Updated last month
- Algorithm For Gene Order Reconstruction in Ancestors☆80Aug 16, 2025Updated 6 months ago
- Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletion…☆26Apr 25, 2018Updated 7 years ago
- Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates…☆44Mar 7, 2024Updated last year
- FastOMA is a scalable software package to infer orthology relationship.☆90Updated this week
- NOVOPlasty - The organelle assembler and heteroplasmy caller☆195Feb 4, 2024Updated 2 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆188May 17, 2024Updated last year
- ☆44Jul 23, 2025Updated 7 months ago
- ASTRAL for PaRalogs and Orthologs☆22Sep 13, 2022Updated 3 years ago
- Genome scaffolding based on HiC data in heterozygous and high ploidy genomes☆60Jan 3, 2025Updated last year
- RNA-seq data amalgamation for a large-scale evolutionary transcriptomics☆12Updated this week
- Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes☆10Oct 16, 2024Updated last year
- SNP and indel calls from multiple sequence alignment (MSA)☆13Nov 11, 2022Updated 3 years ago
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆277Oct 4, 2025Updated 4 months ago
- findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a ske…☆38Jan 16, 2024Updated 2 years ago
- Yet another Hi-C scaffolding tool☆22Oct 23, 2024Updated last year
- Reference-free profiling of polyploid genomes☆141Oct 2, 2025Updated 5 months ago