VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
☆23Oct 21, 2025Updated 4 months ago
Alternatives and similar repositories for VILOCA
Users that are interested in VILOCA are comparing it to the libraries listed below
Sorting:
- ☆19Nov 24, 2025Updated 3 months ago
- Map single-cell transcriptomes to copy number evolutionary trees.☆14Aug 18, 2024Updated last year
- Inference in Bayesian Networks with R☆12Feb 6, 2023Updated 3 years ago
- Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)☆41Feb 24, 2023Updated 3 years ago
- ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and H…☆10May 3, 2018Updated 7 years ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆21Nov 6, 2023Updated 2 years ago
- Front-end code for Serratus project website☆12Jul 2, 2024Updated last year
- A Hierarchical Approach to Pangenomics Inference☆13Apr 15, 2024Updated last year
- ☆25Aug 24, 2025Updated 6 months ago
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆24Feb 22, 2026Updated last week
- ☆12Jul 21, 2025Updated 7 months ago
- This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.☆11Jul 8, 2025Updated 7 months ago
- V-pipe is a pipeline designed for analysing NGS data of short viral genomes☆143Nov 19, 2025Updated 3 months ago
- Gene copy number prediction from k-mer frequencies☆15Jul 29, 2024Updated last year
- A set of Pyro models and functions to infer CNA from scRNA-seq data☆11Aug 14, 2023Updated 2 years ago
- Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.☆14Dec 4, 2025Updated 3 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Computation of average nucleotide identity with the use of MMseqs2☆15Dec 11, 2024Updated last year
- Quality control for phylogenetic analyses☆13Updated this week
- An community curated awesome list of tools, software, databases and other resources for working/analysing RNA Viruses☆21Aug 15, 2025Updated 6 months ago
- ☆17Oct 7, 2024Updated last year
- Variant call verification☆16May 12, 2025Updated 9 months ago
- Prefix-renaming FASTA records really fast.☆17Jun 26, 2024Updated last year
- VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes.☆19Oct 19, 2023Updated 2 years ago
- Single-cell Iso Prep☆17Oct 28, 2023Updated 2 years ago
- Data Structures for Bioinformatics - LM Bioinformatics - University of Rome Tor Vergata☆11Feb 27, 2026Updated last week
- Small pipeline to cluster viral genomes based on their k-mer content. WiP☆17Feb 3, 2026Updated last month
- CellCoal: coalescent simulation of single-cell NGS genotypes☆15Feb 10, 2025Updated last year
- Inverted Repeats Finder: a program to analyze DNA and RNA sequences☆21Feb 21, 2025Updated last year
- A new graphical interface for RAxML☆23Feb 28, 2026Updated last week
- ☆46Nov 21, 2025Updated 3 months ago
- SCASA: Single cell transcript quantification tool☆22Nov 24, 2023Updated 2 years ago
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆27Jul 21, 2025Updated 7 months ago
- Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates☆22Jul 11, 2024Updated last year
- ☆20Feb 12, 2026Updated 3 weeks ago
- A deep learning approach to de novo variant calling in next generation sequencing data☆21Updated this week
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Sep 18, 2019Updated 6 years ago
- a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree