PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees
☆14Apr 15, 2024Updated last year
Alternatives and similar repositories for physpetools
Users that are interested in physpetools are comparing it to the libraries listed below
Sorting:
- A novel bioinformatics pipeline for recent horizontal gene transfer detecting.☆12Nov 13, 2018Updated 7 years ago
- Tool to help visualize data after BLAST by generating pathways on KEGG using an input file of genes and their associated KEGG accession.☆10Apr 29, 2022Updated 3 years ago
- CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification …☆12Mar 20, 2022Updated 3 years ago
- Analyzer of Gene and Species Trees☆10Aug 8, 2016Updated 9 years ago
- ☆13Jan 23, 2020Updated 6 years ago
- Example of SGTK application for E.coli dataset:☆31Jul 13, 2020Updated 5 years ago
- Process consensus file for COG-UK data☆13Sep 7, 2021Updated 4 years ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated 10 months ago
- An easy way of MLSTyping your genomes in R.☆19Dec 21, 2020Updated 5 years ago
- Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.☆19Jul 20, 2018Updated 7 years ago
- Docker images of bioinformatics software☆21Jun 15, 2017Updated 8 years ago
- A parallel API crawler for the retrieval of Kyoto Encyclopedia of Genes and Genomes metabolic and genomics data.☆21Jul 22, 2023Updated 2 years ago
- Mapping-Assisted Targeted-Assembly for Metagenomics☆25Mar 28, 2025Updated 11 months ago
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Sep 23, 2022Updated 3 years ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Jun 4, 2022Updated 3 years ago
- Shiny GUI application for genomics meta-analysis☆22Nov 4, 2020Updated 5 years ago
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆21Aug 31, 2017Updated 8 years ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24May 30, 2024Updated last year
- An efficient way to convert gff3 annotation files into EMBL format ready to submit.☆66Jul 31, 2025Updated 7 months ago
- distance based phylogenetic placement☆27Feb 28, 2024Updated 2 years ago
- Rust bindings to parasail, a SIMD-accelerated pairwise sequence alignment library.☆21Jul 25, 2016Updated 9 years ago
- Pathoscope: Species identification and strain attribution with unassembled sequencing data☆60May 23, 2019Updated 6 years ago
- Tool for demultiplexing Nanopore barcode sequence data☆25Dec 11, 2025Updated 2 months ago
- Indel-aware consensus for aligned BAM☆21Aug 16, 2025Updated 6 months ago
- GenGIS (pronounced 'Genghis' like Genghis Khan) is a bioinformatics application that allows users to combine digital map data with inform…☆29Nov 9, 2017Updated 8 years ago
- ☆23Sep 27, 2019Updated 6 years ago
- Histosketching Using Little Kmers☆56May 25, 2023Updated 2 years ago
- Developments in next generation sequencing: instruments, read lengths, throughput. See☆26Apr 2, 2018Updated 7 years ago
- Dotplot large Genomes in an Interactive, Efficient and Simple way☆113Feb 20, 2026Updated last week
- A phylogeny dating method using least-squares algorithms and criteria☆32Oct 25, 2024Updated last year
- Convert GTDB taxonomy to NCBI taxdump format☆74Aug 24, 2023Updated 2 years ago
- online notebooks for a review of genome sketching☆60Sep 23, 2019Updated 6 years ago
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆34Nov 12, 2020Updated 5 years ago
- K-mer Counting for Biological Sequence Analysis☆28Jan 23, 2026Updated last month
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆74Jul 31, 2025Updated 7 months ago
- FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…☆67Updated this week
- ☆30Sep 21, 2023Updated 2 years ago
- Get microbial sequence data easier and faster☆28Nov 7, 2019Updated 6 years ago