sequence-analysis

Toolkit for processing sequences in FASTA/Q formats

BWK awk modified for biological data

A comprehensive library for computational molecular biology

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

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

Fast alignment and preprocessing of chromatin profiles

Open source bioinformatics and computational biology toolbox written in F#.

A fast multiple sequence alignment program.

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Cython bindings and Python interface to HMMER3.

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.

Tools and software library developed by the ONT Applications group

Sequence alignment tools

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

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

My experimental tools on top of htslib. NOT OFFICIAL!!!

Comprehensive toolkit for generating various numerical features of protein sequences

A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.