santa-dev / santa-simLinks
A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.
☆20Updated 2 years ago
Alternatives and similar repositories for santa-sim
Users that are interested in santa-sim are comparing it to the libraries listed below
Sorting:
- Programmatically interact with the GISAID database.☆80Updated 5 months ago
- Tutorial on Bayesian phylogenetic analysis☆51Updated 8 years ago
- Efficient phylogenetic clustering of viral sequences☆90Updated last month
- Global phylogenies of SARS-CoV-2 sequences☆85Updated 2 years ago
- Python tool to reduce size and redundancy of phylogenetic datasets☆48Updated 3 weeks ago
- Genome wide orthology inference and dNdS estimation☆96Updated 3 months ago
- ☆28Updated 5 years ago
- Reference-guided multiple sequence alignment of viral genomes☆70Updated last month
- R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al., submitted)☆37Updated last month
- Best-fit model selection☆85Updated last year
- MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.☆57Updated 2 months ago
- Reconstruction of transmission trees using genomic data☆70Updated 2 years ago
- Time-resolved metagenomic sequencing of Lenski's long-term evolution experiment with Escherichia coli☆23Updated 6 years ago
- Ancestral character reconstruction and visualisation for rooted phylogenetic trees☆38Updated 2 months ago
- A phylogeny dating method using least-squares algorithms and criteria☆32Updated last year
- Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.☆12Updated 8 years ago
- Rapid analysis and visualization of coronavirus genome variation☆48Updated 3 weeks ago
- Phylogenetic orthology inference for comparative genomics☆80Updated 2 weeks ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Updated 10 months ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆77Updated 5 months ago
- Exploring the "dusk matter" of the RNA virosphere☆35Updated 3 years ago
- SHOOT.bio - the phylogenetic search engine☆27Updated 2 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆51Updated 3 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 6 months ago
- Sydney Phylogenetics Workshop☆68Updated 5 months ago
- MEGAN Community Edition☆72Updated last year
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆81Updated 2 months ago
- CLI tool to annotate genes with KOfam☆87Updated 2 years ago
- An R package designed for drawing gene arrow maps☆95Updated 3 months ago
- Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgam…☆50Updated 7 months ago