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  Multiple Alignment & Phylogeny
  Multiple Alignment
  Editors & Formatters
  Servers & Software for Generating Alignments
2nd Window Opens resource in a 2nd browser window.

2nd Window ALSCRIPT
[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."
[more info][12176]

2nd Window BOXSHADE
[EMBnet.ch+] A program that uses preprocessed multiple alignment files as input to produce printouts of aligned protein or DNA sequences.
[more info][11239]

2nd Window CINEMA
[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.
[more info][10386]

2nd Window GeneDoc
[Pittsburgh Supercomputing Center] GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
[more info][11253]

2nd Window 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.
[more info][12168]

2nd Window JalView
[EBI] A java multiple alignment editor.
[more info][12175]

2nd Window JavaShade
[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."
[more info][12173]

2nd Window 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."
[more info][12170]

2nd Window 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.
[more info][12171]

2nd Window 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.
[more info][12178]

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2nd Window SeaView
[Genetique et Biologie des Populations] This is a multiple sequence alignment editor.
[more info][11280]

2nd Window SeqPup
[Indiana Univ.] A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
[more info][11281]

2nd Window TeXshade
[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."
[more info][12179]

2nd Window Viseur MSF to HTML Conversion Service
(Fabien Campagne) [Annotation pending]
[more info][12174]


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