Editors & Formatters
Bioinformatics & Genomics
Multiple Alignment & Phylogeny
Editors & Formatters
Servers & Software for Generating Alignments
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[EBI] (G.J. Barton) “ALSCRIPT takes a multiple sequence alignment in AMPS block-file format and a set of formatting commands and produces a PostScript file that may be printed on a PostScript laser printer, or viewed using a PostScript previewer.”
[EMBnet.ch+] A program that uses preprocessed multiple alignment files as input to produce printouts of aligned protein or DNA sequences.
[Univ. College London] Cinema allows the building of alignments interactively; either by using a free-format Cut and Paste facility to import a protein or DNA sequence, or by adding sequences directly from the OWL composite database. Alternatively, alignments may be loaded from the PRINTS fingerprint database and again may be customized by the addition of user-defined or OWL sequences.
[Pittsburgh Supercomputing Center] GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
Genetic Data Environment
[Bioinformatics and Molecular Analysis Section – NIH] This is a manual and guide on how to use the Genetic Data Environment software, which is an expandable GUI for multiple sequence analysis.
[EBI] A java multiple alignment editor.
[EBI] “JavaShade is an interactive drawing program for preparing previously-generated multiple sequence alignments for publication, and for looking at
the conservation of residues across the alignment.”
MACAW ftp Site
[NCBI] “MACAW is a program for locating, analyzing, and editing blocks of localized sequence similarity among multiple seqences and linking them into a composite multiple alignment.”
ProMSED2 and ViSEd1.1 ftp Site
[Indiana University] At this ftp site, users may download ProMSED2 and ViSEd1.1 which are both muliple sequence alignment editors for the Windows platform.
Protein Sequence and Multiple Alignment Sequence Colourer
[Weizmann Institute] (STING paint) STING paint allows for the presentation of residue characteristics in the Sequence
Frame and Multiple Sequence Alignment (MSA) coloring.
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[Genetique et Biologie des Populations] This is a multiple sequence alignment editor.
[Indiana Univ.] A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
[University of Tuebingen] “TeXshade is an alignment shading software completely written in TeX/LaTeX which can process multiple sequence alignments in the .MSF and the .ALN file format. It provides in addition to common shading algorithms special shading modes featuring functional aspects, e.g. charge or hydropathy, and a plenitude of commands for handling shading colors, text styles, labels, legends and even allows the user to define completely new shading modes.”
Viseur MSF to HTML Conversion Service
(Fabien Campagne) [Annotation pending]