neherlab / treetime_examplesLinks
A collection of documented examples using TreeTime
☆22Updated 6 years ago
Alternatives and similar repositories for treetime_examples
Users that are interested in treetime_examples are comparing it to the libraries listed below
Sorting:
- Python bindings for the TaxonKit library☆41Updated last month
- Add biological annotations to variants in a given VCF file.☆32Updated 4 years ago
- MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.☆57Updated 2 months ago
- BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale☆56Updated 2 years ago
- create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks☆57Updated last month
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Updated last month
- ☆26Updated 2 years ago
- Reference-guided multiple sequence alignment of viral genomes☆70Updated 2 months ago
- SHOOT.bio - the phylogenetic search engine☆27Updated 2 years ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Updated 3 months ago
- OPAL: Open-community Profiling Assessment tooL☆30Updated this week
- map Illumina metagenomes to genomes!☆38Updated last month
- A package to annotate protein sequences☆60Updated 10 months ago
- Influenza genome analysis Nextflow workflow☆31Updated 3 months ago
- Visualization of the pan-genome output by panX☆65Updated 6 months ago
- A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies☆35Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Updated last year
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆64Updated last year
- ☆43Updated last year
- Bacterial Annotation by Learned Representation of Genes☆58Updated 4 years ago
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆48Updated 3 weeks ago
- Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.☆26Updated 7 years ago
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆25Updated 2 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆35Updated 4 years ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆55Updated 6 months ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆45Updated this week
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆37Updated last year
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- Influenza genome analysis Nextflow workflow☆24Updated this week
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆71Updated last month