Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions
☆71Oct 16, 2023Updated 2 years ago
Alternatives and similar repositories for PhyloCSF
Users that are interested in PhyloCSF are comparing it to the libraries listed below
Sorting:
- PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…☆31Jan 26, 2022Updated 4 years ago
- Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.☆109Jun 17, 2022Updated 3 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 6 months ago
- A JBrowse 1 plugin to view multiple alignment format (MAF) files☆27Oct 25, 2023Updated 2 years ago
- Newick tree processing☆13Feb 22, 2026Updated last week
- Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit☆11Jan 17, 2020Updated 6 years ago
- Find and visualize rearrangements in DNA sequences☆55Dec 1, 2025Updated 3 months ago
- Tools for improving the sensitivity and specificity of genome alignments☆58Jan 17, 2024Updated 2 years ago
- Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.☆56Updated this week
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- BITACORA: A Bioinformatics tool for gene family annotation☆53Dec 10, 2025Updated 2 months ago
- The MafFilter genome alignment processor☆19Jan 6, 2026Updated last month
- ☆30Aug 1, 2023Updated 2 years ago
- VESPA: Very large-scale Evolutionary and Selective Pressure Analyses☆15Mar 18, 2022Updated 3 years ago
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Sep 18, 2019Updated 6 years ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆39Sep 22, 2025Updated 5 months ago
- Gap2Seq is a gap filling and insertion genotyping tool.☆22Aug 12, 2024Updated last year
- DNA multiple sequence aligner, official version from Penn State's Miller Lab☆36Mar 27, 2019Updated 6 years ago
- PhyloAcc a software to detect the changes of conservation of a genomic region☆35Feb 4, 2026Updated 3 weeks ago
- RegCloser is a genome gap-closing tool based on the robust regression approach, which is conceptually applicable to de novo assembly of N…☆15Apr 22, 2024Updated last year
- source code for EVM☆122Nov 29, 2024Updated last year
- Annotate Olfactory receptor CDS from genome☆10Apr 29, 2023Updated 2 years ago
- Just Annotate My Genome☆19Sep 17, 2024Updated last year
- FastK based version of Merqury☆32Jan 19, 2026Updated last month
- ☆73Jun 2, 2023Updated 2 years ago
- The RepeatScout 1.0.5, written by Pevzner et al., source code for browsing. The official release and more information are available at h…☆16Apr 14, 2023Updated 2 years ago
- PHAST☆82Feb 20, 2026Updated last week
- Haplotype aware de novo assembly of diploid genome from long reads☆54Mar 16, 2022Updated 3 years ago
- Synteny Mapping and Analysis Program☆30Feb 14, 2026Updated 2 weeks ago
- ☆26Updated this week
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 2 years ago
- ☆10Jun 13, 2020Updated 5 years ago
- KAUST Assembly Read Error Correction Tool☆15Aug 15, 2015Updated 10 years ago
- A nextflow pipeline for polishing CLR assemblies☆18Feb 3, 2023Updated 3 years ago
- Scotch pipeline for indel calling.☆10Nov 25, 2019Updated 6 years ago
- EM-PCA for Ultra-low Coverage Sequencing Data☆18Dec 18, 2025Updated 2 months ago
- Plot CNV data with a genome viewer in R☆15Apr 5, 2017Updated 8 years ago
- 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
- Hierarchical Alignment Format☆174Jan 23, 2026Updated last month