PREQUAL: a pre-alignment quality filter for comparative sequence analyses
☆33Jun 1, 2022Updated 3 years ago
Alternatives and similar repositories for prequal
Users that are interested in prequal are comparing it to the libraries listed below
Sorting:
- 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
- The BaitFisher-package is a software package for designing hybrid enrichment probes. For more information see:☆13Oct 20, 2021Updated 4 years ago
- Package to plot phylogenies with custom shapes☆24Apr 17, 2024Updated last year
- Two-dimensional outlier detection algorithm for pinpointing errors in small species-specific stretches of the multiple sequence alignment…☆16May 27, 2024Updated last year
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated 10 months ago
- ☆16Feb 20, 2024Updated 2 years ago
- Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)☆14Sep 17, 2022Updated 3 years ago
- Codon-Aware Multiple Sequence Alignments☆20Nov 15, 2024Updated last year
- A massively parallel tool for model selection and tree inference on thousands of genes☆51Mar 4, 2024Updated 2 years ago
- Script to help assessing the evolutionary history of a TE family☆16Sep 5, 2019Updated 6 years ago
- SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event.☆24Sep 23, 2024Updated last year
- Calculate summary statistics and manipulate multiple sequence alignments☆91Jan 28, 2026Updated last month
- Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO☆13Oct 30, 2018Updated 7 years ago
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Mar 5, 2018Updated 8 years ago
- CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on c…☆10Jun 9, 2022Updated 3 years ago
- A program for divvying or partially filtering multiple sequence alignments☆27Oct 14, 2019Updated 6 years ago
- Tools for working with second gen assemblies, fasta sequences, etc☆95Sep 8, 2016Updated 9 years ago
- Python-interface C++ library for Bayesian phylogenetics via optimization☆41Apr 8, 2024Updated last year
- ☆17Feb 16, 2026Updated last month
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆82Updated this week
- A high performance tool to identify orthologs and paralogs across genomes.☆27Mar 8, 2023Updated 3 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
- Gene Family Annotation Workflow☆11Mar 26, 2024Updated last year
- ☆16May 7, 2023Updated 2 years ago
- Code to perform homolog detectability analyses as described in Weisman et al. 2020 (https://www.biorxiv.org/content/10.1101/2020.02.27.96…☆18Nov 18, 2024Updated last year
- ☆78Jun 2, 2025Updated 9 months ago
- PhyloAcc a software to detect the changes of conservation of a genomic region☆35Feb 4, 2026Updated last month
- An R framework for phylostratigraphy☆35Aug 12, 2025Updated 7 months ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 3 years ago
- Data and scripts used in the oneKP capstone analyses☆13Apr 5, 2022Updated 3 years ago
- Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding☆20Mar 3, 2025Updated last year
- haplotypic duplication identification tool☆277Oct 30, 2025Updated 4 months ago
- ☆15Oct 9, 2025Updated 5 months ago
- Reference genome quality scores☆20Dec 17, 2020Updated 5 years ago
- Accurate Species TRee ALgorithm☆275Apr 1, 2024Updated last year
- ☆13Nov 15, 2017Updated 8 years ago
- ☆18Nov 9, 2020Updated 5 years ago
- Tutorials and materials for planning a HybSeq project, processing sequences, and conducting phylogenomic analyses.☆16May 19, 2017Updated 8 years ago
- BOSTIn is a new, user-friendly phylogenetic artifact identification package.☆11Jan 20, 2026Updated 2 months ago