(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

Sequence Alignment Visualization

Proteomics

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

Keywords:

Protein Structure Analysis

Proteomics

(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:

High-throughput sequencing

Proteomics

Proteomics

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

Protein Structure Analysis

Proteomics

Proteomics

Other

fast and flexible semi-supervised learning for peptide detection.

Keywords:

Proteomics

Proteomics

a tool to integrate a number of Shotgun proteomics tools, generating ready to use result files.

Keywords:

Proteomics

Proteomics

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

a suite of tools for processing of metabolomics data.

Keywords:

Metabolic Network Analysis

Proteomics