STAG: Species Tree from All Genes
☆36Dec 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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- STRIDE: Species Tree Root Inference from Gene Duplication Events☆10Aug 28, 2018Updated 7 years ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated last year
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆46Nov 21, 2019Updated 6 years ago
- The final version 2 release of our software to detect core genes in eukaryotic genomes☆30Mar 31, 2015Updated 11 years ago
- Analyzing combinations of codon substitution histories☆46Apr 7, 2026Updated 3 weeks ago
- 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.
- Implementation of the TreeShrink problem☆55Apr 22, 2026Updated last week
- Version 5 of the CAFE phylogenetics software☆165Mar 16, 2026Updated last month
- 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
- 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 10 months ago
- Fast, accurate species tree estimation.☆12Aug 29, 2024Updated last year
- SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity …☆95Apr 23, 2026Updated last week
- Extensive de-novo TE Annotator☆444Apr 5, 2026Updated 3 weeks ago
- Some useful bioinformatics pipelines for genomics analysis☆14May 25, 2021Updated 4 years ago
- use paired-end transcriptome reads to scaffold genomes☆11May 30, 2019Updated 6 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 7 years ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆57Jan 26, 2023Updated 3 years ago
- Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees/networks)☆20Apr 25, 2026Updated last week
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.☆19Apr 24, 2024Updated 2 years ago
- Accurate Species TRee ALgorithm☆277Apr 1, 2024Updated 2 years ago
- orthology assignment using phylogenetic and network analyses☆55Jan 21, 2026Updated 3 months ago
- ☆237Jan 24, 2025Updated last year
- Automated de novo assembly of whole chloroplast genomes.☆48Sep 23, 2024Updated last year
- A program to call variants from genome alignment☆83Apr 29, 2025Updated last year
- 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.
- Helper scripts for making phylogenies☆15Jun 7, 2024Updated last year
- An R package to infer and analyze synteny networks from protein sequences☆38Jul 23, 2025Updated 9 months ago
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆241Updated this week
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year
- Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletion…☆26Apr 25, 2018Updated 8 years ago
- FastOMA is a scalable software package to infer orthology relationship.☆96Apr 24, 2026Updated last week
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆30Feb 23, 2026Updated 2 months ago
- Clann: Investigation of phylogenomic signal using supertrees☆18Apr 21, 2026Updated last week
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆20Jun 20, 2022Updated 3 years ago
- Scatterbar - data visualization for proportional data across many spatially resolved coordinates☆11Mar 3, 2025Updated last year
- TransDecoder source☆304Mar 22, 2026Updated last month
- Estimating gene family turnover rates by likelihood-based methods☆12Aug 17, 2020Updated 5 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated last year
- Phylogenetic orthology inference for comparative genomics☆854Jul 15, 2025Updated 9 months ago
- PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics☆38Apr 28, 2023Updated 3 years ago