ALTEMO is a package of functions written in Python for bioinformatics proposed as a final project in the course of Algorithmic Techniques and Models (325) at the University of Málaga.
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Updated
Nov 30, 2021 - Python
ALTEMO is a package of functions written in Python for bioinformatics proposed as a final project in the course of Algorithmic Techniques and Models (325) at the University of Málaga.
instructions, python and R code for generating lava lamp plots of kmer coverage
K-Mer management tools
A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage in Parallel
This is our implementation for D2 distance algorithm for k-mers.
A naive implementation of a k-mer counter in Python, takes fasta files and k-mer length requests and outputs all k-mers of length k, their reverse complement, and their frequency within their respective sequence for each sequence in the file.
A kmer-based homology searching tool
Count canonical kmers with Emil Ernerfeldt's emilib::HashMap
Collapse a set of redundant kmers to use IUPAC degenerate bases
Decompose a k-mer profile into several peaks each representing a copy number.
A C and Python implementation of latent strain analysis for eigengenome partitioning.
Count canonical kmers with STL unordered_map
Repo for code and data related to project developing methodology for applying Harmonic Mean P-Values to sliding windows of multiple aligned genomes.
Count canonical kmers with Malte Skarupke's bytell_hash_map hash table
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