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)
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.
https://github.com/brentp/spacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
https://github.com/broadinstitute/g2papi
Python Client Library for the G2P Portal API
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/cdcgov/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
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.
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