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Projects in Awesome Lists tagged with sequence-analysis

A curated list of projects in awesome lists tagged with sequence-analysis .

https://github.com/lh3/seqtk

Toolkit for processing sequences in FASTA/Q formats

bioinformatics sequence-analysis

Last synced: 15 May 2025

https://github.com/biotite-dev/biotite

A comprehensive library for computational molecular biology

bioinformatics computational-biology pdb-files sequence-analysis structural-biology

Last synced: 22 Jan 2026

https://github.com/lh3/bioawk

BWK awk modified for biological data

bioinformatics sequence-analysis

Last synced: 12 Apr 2025

https://github.com/seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

bioinformatics blast cpp-concepts cpp20 fasta fastq fm-index modern samtools seqan sequence-alignment sequence-analysis

Last synced: 15 May 2025

https://github.com/haowenz/chromap

Fast alignment and preprocessing of chromatin profiles

bioinformatics chromatin-profiles genomics sequence-analysis

Last synced: 09 May 2025

https://github.com/lh3/readfq

Fast multi-line FASTA/Q reader in several programming languages

bioinformatics sequence-analysis

Last synced: 07 May 2025

https://github.com/moshi4/pymsaviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

bioinformatics genomics matplotlib msa multiple-sequence-alignment python sequence-alignment sequence-analysis visualization

Last synced: 07 May 2025

https://github.com/yuanx749/py-cdhit

A Python package for CD-HIT, clustering protein or nucleotide sequences.

bioinformatics package sequence-analysis tool

Last synced: 09 Aug 2025

https://github.com/Superzchen/iLearnPlus

iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences.

automated-modelling bioinformatics-tool biomedical-data-analytics deep-learning feature-selection machine-learning prediction python sequence-analysis

Last synced: 21 Jul 2025

https://github.com/althonos/peptides.py

Physicochemical properties, indices and descriptors for amino-acid sequences.

bioinformatics protein pure-python qsar-models sequence-analysis

Last synced: 10 Apr 2025

https://github.com/ggonnella/gfapy

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

assembly bioinformatics gfa graphs sequence-analysis

Last synced: 05 Apr 2025

https://github.com/nanxstats/protr

🧬 Toolkit for generating various numerical features of protein sequences

bioinformatics feature-engineering feature-extraction machine-learning peptides protein-sequences sequence-analysis

Last synced: 09 Sep 2025

https://github.com/althonos/lightmotif

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

bioinformatics genomics pssm rust-library sequence-analysis sequence-motif simd

Last synced: 04 Oct 2025

https://github.com/edinburgh-genome-foundry/geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

python sequence-analysis synthetic-biology

Last synced: 02 Jul 2025

https://github.com/soedinglab/spacepharer

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

bioinformatics crispr host-pathogen sequence-analysis

Last synced: 27 Apr 2025

https://github.com/sysbiochalmers/hgtphylodetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

evolutionary-biology high-throughput-pipeline horizontal-gene-transfer phylogenetics sequence-analysis systems-biology

Last synced: 29 Jul 2025

https://github.com/ylab-hi/pxblat

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

alignment bioinformatics blat c cpp pybind11 python sequence-analysis

Last synced: 14 Jan 2026

https://github.com/incertae-sedis/smof

Explore and analyze biological sequence data

bioinformatics biology fasta genomics sequence sequence-analysis

Last synced: 17 Dec 2025

https://maraab23.github.io/ggseqplot/

R library for visualizing (social science) sequence data using ggplot2

ggplot2 r r-package rstats sequence-analysis traminer visualization

Last synced: 06 May 2025

https://github.com/maraab23/ggseqplot

R library for visualizing (social science) sequence data using ggplot2

ggplot2 r r-package rstats sequence-analysis traminer visualization

Last synced: 15 Apr 2025

https://github.com/ebedthan/sabreur

fast, reliable and handy demultiplexing tool for fastx files

bioinformatics demultiplexing rust sequence-analysis

Last synced: 15 Sep 2025

https://github.com/althonos/pymemesuite

Cython bindings and Python interface to the MEME suite, a collection of tools for the analysis of sequence motifs.

bioinformatics cython-library genomics meme-suite sequence-analysis sequence-motif

Last synced: 21 Mar 2025

https://github.com/mbhall88/classification_benchmark

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification

bioinformatics contamination sequence-analysis taxonomic-classification tuberculosis

Last synced: 11 Apr 2025

https://github.com/mt1022/cubar

R Package for Codon Usage Bias Analysis. Comprehensive documentation and tutorials are available at:

bioinformatics codon-usage machine-learning r-package sequence-analysis

Last synced: 22 Oct 2025

https://github.com/sib-swiss/pftools3

A suite of tools to build and search generalized profiles

motif profile protein-domains sequence-analysis

Last synced: 14 Apr 2025

https://github.com/althonos/pyncbitk

Cython bindings and Python interface to the NCBI C++ ToolKit (including BLAST+).

bioinformatics blast cython-library python-bindings python-library sequence-analysis

Last synced: 30 Dec 2025

https://github.com/nbisweden/contigtax

Taxonomic classification of metagenomic contigs

metagenomics metatranscriptomics sequence-analysis taxonomy-assignment

Last synced: 05 Mar 2025

https://github.com/weekend37/string-kernels

Implementation of the Polynomial String Kernel and linear time String Kernel implementation. Compatible and ready for easy plug-in to Scikit-Learn's Support Vector Machines and supports multithreading.

algorithms genomics kernelsvm machine-learning multithreading sequence-analysis

Last synced: 14 Jan 2026

https://github.com/nmdp-bioinformatics/seq-ann

Python package for doing fast and accurate sequence annotation

bioinformatics gfe hla hla-typing ngs sequence-analysis

Last synced: 28 Jan 2026

https://github.com/intervals-mining-lab/libiada-core

The classes library for analysis of large data arrays, based on new approach in the field of informatics - formal order analysis (FOA).

bioinformatics c-sharp formal-order-analysis informatics information-theory mathematical-linguistics sequence-analysis

Last synced: 17 Dec 2025

https://github.com/ioangatop/datamining

Data Mining techniques on predicting mood using time-series analysis in mental health and predicting the click behaviour of users in a hotel ranking system.

data-mining data-science prediction ranking-algorithm sequence-analysis xgboost

Last synced: 24 Dec 2025

https://github.com/feldroop/genedex

A small and fast FM-Index for Rust

bioinformatics data-structures fmindex search sequence-analysis

Last synced: 13 Sep 2025

https://github.com/jeanmanguy/kappa-casein-evolution-paper

Code for the analysis and figures for the paper: Manguy J, Shields DC. Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles. Royal Society Open Science. 2019 Oct 16;6(10):190939. Available from: https://royalsocietypublishing.org/doi/10.1098/rsos.190939

bioinformatics biology casein evolution milk protein r rstats sequence-analysis

Last synced: 22 Jun 2025

https://github.com/nsbuitrago/vfind

Simple variant finding from NGS data

bioinformatics ngs sequence-analysis

Last synced: 02 Feb 2026

https://github.com/mullinslab/methylation-station

An application for analyzing and visualizing DNA methylation in multiple sequence alignments

bioinformatics methylation sequence-analysis visualization

Last synced: 30 Oct 2025

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.

bioinformatics cdc-influenza-division data-cleaning data-normalisation data-normalization data-science fasta ncird ncird-id sequence-alignment sequence-analysis sequence-annotation

Last synced: 15 Apr 2025

https://github.com/xapple/seqsearch

Sequence similarity searches (e.g. BLAST) made easy

bioinformatics blast-search database-management sequence-analysis

Last synced: 27 Dec 2025

https://github.com/rajesh26k/two-row-arrays

Recursive integer array transformation system inspired by mathematical pattern analysis.

colab frequency-analysis java mathematics pattern-detection sequence-analysis

Last synced: 21 Aug 2025

https://github.com/mvinyard/seq-toolkit

Basic functions for genomic sequence manipulation

dna-sequences genomics sequence-analysis

Last synced: 26 Jul 2025

https://github.com/leonardogemin/duohash

DuoHash is an advanced tool for the efficient calculation of forward and reverse hashes of spaced k-mers in nucleotide sequences, improving the analysis of genomic data by reducing processing time and computational resources.

algorithm-optimization bioinformatics computational-biology dna-sequencing genomics hashing sequence-analysis spaced-kmer

Last synced: 06 Dec 2025

https://github.com/berraylvc/bioseq-analyzer

DNA FASTA sequence analyzer built with Biopython

bioinformatics biopython cli fasta python sequence-analysis

Last synced: 24 Dec 2025

https://github.com/gauravcodepro/evolutioncal

A evolutionary function in ruby which given a similarity score means the number of the similar bases and the dissimilar bases and then the sequence rate and the divergence rate calculates a ratio which can tell us how much sequencing depth to be covered

evolution evolutionary-computation evolutionary-strategy ruby rubyprogramming sequence-analysis

Last synced: 22 Feb 2025

https://github.com/gauravcodepro/plant-resistance-gene-fetcher

a custom function to fetch the dna and the protein sequence from the plant resistance gene database and get the corresponding dna_sequence and the protein_sequence.

bioinformatics disease-detection diseaseresistance plantgenomics plantresistance sequence-analysis sequence-labeling

Last synced: 22 Feb 2025

https://github.com/ctskennerton/fx_tools

Very small utilities for interrogating fasta and fastq files

bioinformatics fasta fastq sequence-analysis

Last synced: 02 Apr 2025