tcfinder
A lightweight tool to find clusters of samples within a phylogeny.
This command-line tool finds clusters of tips from a list of identifiers within a phylogeny in tabular phylo4 format (see phylobase), regarding a minimum cluster size and a minimum proportion of targets in the cluster.
Basic Information
| Repository | https://github.com/PathoGenOmics-Lab/tcfinder |
| Documentation | https://github.com/PathoGenOmics-Lab/tcfinder/blob/main/README.md |
| Main publication (DOI) | 10.1093/ve/veaf015 view |
| Contact email | pathogenomic@uv.es |
| Authors/Maintainers | Miguel Álvarez Herrera |
| Type of application | Conda package, Package for compiling the executable program |
| Programming languages | Rust |
| Keywords | Computational Methods, Molecular evolution, Phylogenetic Analysis |
Technical details
| Input file formats | csv |
| Output file formats | csv |
| Software compatibility | Linux, Mac, Windows |
| Hardware requirements | No specific hardware requirements |
| Type of containerization | Conda |
| Wrapper type | None |
| Compatible tools | phylobase |
| Funding resource | National competitive funding, Regional/local competitive funding |
| Funding support | Regional/local competitive funding |
Statistics
| Unique users (last 12 months) | |
| Unique users (since first release) | |
| Software downloads (last 12 months) | |
| Software downloads (since first release) | 694 |
| Jobs submitted (last 12 months) | |
| Jobs submitted (since first release) | |
| Repository clones (last 12 months) | |
| Repository clones (since first release) | |
| Citations (last 12 months) | <100 (~0 as of 15/10/2026) |
| Citations (since first release) | <100 (2 as of 15/10/2026) |
| Early-stage researcher effort (development) | 1 |
| Early-stage researcher effort (maintenance) | 1 |
| Technician-supported effort (development) | |
| Technician-supported effort (maintenance) | |
| Other effort (development) | |
| Other effort (maintenance) | |
| Total effort (development) | 1 |
| Total effort (maintenance) | 1 |