libdna
samtools
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libdna
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A good, fast hash for nucleotides triplet converted to 0, 1, 3, 2 using `3 & (nuc << 1)`
While that works for the canonical bases your method won't support CCN which should give Proline. Hence, for my implementation I have opted for a slower but more general approach. As protein coding sequences are usually short performance isn't an issue, really.
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Counting the number of matching characters in two ASCII strings
In Bioinformatics, if you now the number of mismatching characters between two strings of DNA your can compute their evolutionary distance. As DNA is long, easily a few megabytes, computing such a hamming distance via SIMD really pays of. Here is my implementation if anyone is interested: https://github.com/kloetzl/libdna
samtools
We haven't tracked posts mentioning samtools yet.
Tracking mentions began in Dec 2020.
What are some alternatives?
htslib - C library for high-throughput sequencing data formats
Genbank - Genbank format tools and parser
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
ViennaRNAParser
pn2codon - Python Rust FFI for reverse-translating Amino Acid sequences to DNA sequences
seqtk - Toolkit for processing sequences in FASTA/Q formats
ProteinToCodonTranslator
RNAlien - RNAlien - unsupervised RNA family model construction
phybin - Binning (Newick) Phylogenetic Trees by Topology
BlastHTTP - Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice
ADPfusionForest - Dynamic programming on tree and forest structures
vcf - Haskell library to handle VCF (Variant Call Format) files