(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.

Keywords:

Comparative Genomics

Genomics

Proteomics

Sequence Alignment Visualization

a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.

Keywords:

Proteomics

Protein Structure Analysis

(Fast and Accurate Multiple Sequence Aligner) implements an algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM).

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

Keywords:

Proteomics

Proteomics

High-throughput sequencing

is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

Keywords:

Multiple Structure Alignment

Proteomics

Protein Structure Analysis

Proteomics

Other

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.

Keywords:

Proteomics

Proteomics

semi-supervised learning for peptide identification from shotgun proteomics datasets.

Keywords:

Proteomics

Proteomics