Applied Computational Genomics Team's repositories
ProGraphMSA
ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. Fork of ProGraphMSA+TR from https://sourceforge.net/projects/prographmsa
webSTR-API
WebSTR-API: programmatic access to WebSTR, database of Human genome-wide variation in Short Tandem Repeats (STRs)
rust-phylo
Phylo library in Rust
rust-indelMaP
IndelMaP algorithm implementation in Rust
swissrepeats
Delucchi, M.; Schaper, E.; Sachenkova, O.; Elofsson, A.; Anisimova, M. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes 2020, 11, 407.
twins_microbiome_pipeline
Bioinformatics processing of raw Illumina reads for microbiome analysis of twins (dada2)
IndelViewer
Indel viewer software for ARPIP
single-char-indel-ASR-preserves-long-indels
This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestral reconstruction of multiple-character indels under the PIP.
armrppipeline
Collection of scripts for analyzing Armadillo repeat proteins
Bioinfo4B-STR
Short tandem repeat project for the course "Bioinformatics for Beginners"
JATI
Initial attempt at JATI in Rust
primate_SLC6A3
Annotation of variable number tandem repeats (VNTRs) in primate SLC6A3 genes
STRs-in-CRC
Notebooks and scripts for the analysis of short tandem repeat mutations in colorectal cancer data
TRAL-Result-Analysis
R package to get the most out of the results from TRAL
tral-visualization
Code for visualizing TRAL results