List of alignment visualization software: Difference between revisions

Revision as of 06:46, 15 July 2010

Revision as of 14:22, 11 August 2010

Line 44:

| No

| Dotplot, 6 frame translation, Blast

| [[Nexus formatfile|NEXUSNexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[PIR format|PIR]], PRINTS

| Free

| [http://www.bioinf.manchester.ac.uk/dbbrowser/CINEMA2.1/ link]

Line 62:

| [[Neighbor-joining]]

| Alignment quality analysis

| [[Nexus formatfile|NEXUSNexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]]

| Free for academic users

| [http://www.clustal.org/ link]

Line 71:

|

| can compute several population genetics statistics, reconstruct haplotypes with PHASE

| [[FASTA]], [[NEXUSNexus file|Nexus]], Mega, [[PHYLIP]]

| [[Freeware]]

| [http://www.ub.es/dnasp/ link]

Line 134:

| [[Neighbor-joining]]

| Manual annotation, conservation scores

| [[Nexus formatfile|NEXUSNexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], PFAAT

| Free

| [http://pfaat.sourceforge.net/ link]

Line 161:

| No

| Dot-plot, [[vim]]-like editing keys

| [[Nexus formatfile|NEXUSNexus]], [[MSF format|MSF]], [[Clustal]], [[FASTA format|FASTA]], [[PHYLIP format|PHYLIP]], [[MASE format|MASE]]

|

| [http://pbil.univ-lyon1.fr/software/seaview.html link]

Line 179:

| [[Neighbor-joining]]

| Dot-plot, Structure-neighbors, 3D-superposition, Blast-search, Mutation/SNP analysis, Sequence features, [[Biojava]]-interface

| [[MSF]], [[Stockholm format|Stockholm]], [[Clustal]]w, [[Nexus file|Nexus]], [[FASTA]], [[PDB]], Embl, [[GenBank]], [[hssp]], [[Pfam]]

| [[GPL]]

| [http://3d-alignment.eu/ link]