List of alignment visualization software: Difference between revisions

Revision as of 23:51, 20 June 2021

Revision as of 17:32, 5 November 2021

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| [[Jalview]]

| {{yes|Secondary structure prediction via [http://www.compbio.dundee.ac.uk/~www-jpred/ JNETJPred 4]}}

| {{yes|[[Clustal#Clustal_Omega|Clustal O]], [[Clustal]], GLprobs, MSAprobs, [[MUSCLE (alignment software)|MUSCLE]], [[MAFFT]], Probcons, TCoffee, via web services}}

| {{yes|[[UPGMA]], [[Neighbor joining|NJ]]}}

| Sequences and features retrieved from user-configurable and publicly registered servers, e.g. [[European_Molecular_Biology_Laboratory|EMBL]], [[European_Bioinformatics_Institute|EBI]], [[Protein_Data_Bank|PDB]], [[Pfam]], [[Rfam]], [[UniProt]] Accession retrieval. Structure/model data retrieval from [[Protein_Data_Bank|PDB]] and 3D-Beacons including [[Protein_Data_Bank|PDBe]], [[AlphaFold#Protein_Structure_Database|AlphaFold DB]], [[Swiss-model|SWISS-MODEL]].

| Sequences and features from arbitrary and publicly registered [[Distributed Annotation System|DAS]] servers, PFAM, PDB, EMBL, Uniprot Accession retrieval.

| [[FASTA format|FASTA]], [[PFAM format|PFAMPfam]], MSF, [[Clustal]], [[BLC format|BLC]], [[Protein Information Resource|PIR]], [[Stockholm format|Stockholm]], [[Variant_Call_Format|VCF]], AMSA, BioJSON, Clustal, [[European_Nucleotide_Archive#EMBL-Bank_format|ENA]], [[GenBank]], [[General_feature_format|GFF2]], [[General_feature_format|GFF3]], JnetFile, [[PHYLIP]], [[Pileup_format|PileUp]], RNAML, [[Crystallographic_Information_File|CIF]], [[Crystallographic_Information_File|mmCIF]], [[Protein_Data_Bank_(file_format)|PDB]].

| {{free}}, [[GNU General Public License|GPL]]

|[https://www.jalview.org/jalview-js/ JalviewJS] (Javascript)

|Applet

|Cross-platform -Mac OSmacOS, Linux, Windows, other with Java Virtual Machine.

| {{Official website|https://www.jalview.org/}}

Windows

| {{Official website|www.jalview.org}}

|-

| Jevtrace