Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer
Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer - Published in JOSS (2019)
org.biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
helayo
helayo: Reconstructing Sanskrit texts from manuscript witnesses - Published in JOSS (2022)
biopython
Official git repository for Biopython (originally converted from CVS)
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
filtersam
Tools to filter SAM/BAM files by percent identity and percent of matched sequence
https://github.com/althonos/pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
https://github.com/althonos/pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
pymsaviz
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
https://github.com/althonos/pymuscle5
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
polya
Automatically Adjudicate Any And All Arbitrary Annotations, Astutely Adjoin Abutting Alignments, And Also Amputate Anything Amiss (AAAAAAAAAAAAAAAA)
https://github.com/brentp/spacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
https://github.com/cdcgov/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
https://github.com/biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
https://github.com/benhid/pymsa
Scoring multiple sequence alignments with Python
ssw
🚀 R interface for SSW, a fast implementation of the Smith-Waterman algorithm using SIMD
https://github.com/broadinstitute/g2papi
Python Client Library for the G2P Portal API
https://github.com/cdcgov/clean-genes
A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.
goombay
Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.