Multiple Sequence Alignment
- POA 2 – Multiple Sequence Alignment Using Partial Order Graphs
- SPLICE POA 20040610 – Splice Analysis using Partial Order Multiple Sequence Alignment
- Entropy Calculator 3.3.1 – Multiple Sequence Alignment Scoring
- JProfileGrid 2.0.5 – Multiple Sequence Alignment tool that generates ProfileGrids
- PICS-Ord 20110823 – Extract Phylogeny Information from hard-to-align Regions of Multiple Sequence Alignments
- STACCATO 1.2 – Structure Based Multiple Sequence Alignment
- ProGraphMSA – Fast and Robust Phylogeny-Aware Multiple Sequence Alignment
- MSACompro 1.2.0 – Protein Multiple Sequence Alignment using predicted Secondary Structure
- PCMA – Profile Consistency Multiple sequence Alignment
- Clustal Omega 1.1.0 – Multiple Sequence Alignment
- MSAProbs 0.9.7 – Parallel and Accurate Multiple Sequence Alignment
- PCPMer 3.5.6 – Determine Conserved Regions in multiple Sequence Alignments
- T-Coffee 9.03 – Multiple Sequence Alignment Tools
- KAlignmentViewer 20050624 – Interface for Display and Browsing of Multiple Sequence Alignments
- PSAR – Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling
- PFAAT 2.0 – Multiple Sequence Alignments Analysis
- MultAlin 5.4.1 – Multiple Sequence Alignment
- AQUA 1.1 – Automatic Quality Improvment for Multiple Sequence Alignment
- PRRN 3.5.2 – Multiple Sequence Alignment by Doubly Nested Randomized Iterative Method
- xalign 6.1 – Multiple Sequence Alignment
- Probalign 1.4 – Multiple Sequence Alignment
- RNAstrand 2.0.0 – Predict Reading Direction of Structured RNAs in Multiple Sequence Alignments
- noisy 1.5.12 – Identify Homo-plastic Characters in Multiple Sequence Alignments
- Gmaj 20081103 – Interactive Viewer for Multiple Sequence Alignments
- Anchored DIALIGN 2.2.2 – Multiple Sequence Alignment with User-defined Constraints
- MUSCLE 3.8.31 – Multiple Sequence Alignment
- OMA 1.0 – Optimal Multiple Sequence Alignment
- DCA 1.1 – Divide-and-Conquer Multiple Sequence Alignment
- Dialign 2.2.1 / DIALIGN-TX 1.0.2 – Multiple Sequence Alignments
- OXBench 1.3 – Evaluate Accuracy of Protein Multiple Sequence Alignment
- AlScript 2.0 – Format Multiple Sequence Alignments in PostScrip
- Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 – Multiple Sequence Alignment , Viewer & Quality Assessment
- POAVIZ – Partial Order Multiple Sequence Alignment Visualizer
- ClustalW / ClustalX 2.1 – Multiple Sequence Alignment


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