This page is very out of date! Many links below still work, but for a more
current depiction see SAF Resources.
These are still relevant:
SAF Software Documentation
This page contains links to an assortment of online documentatation for
the software present on SAF computers.
General Information refers primarily to programs
that are standard parts of the computer's operating system.
SAF specific software has been
installed in addition to the standard operating system - these are primarily
tools that may help
SAF users carry out their research.
Updated 04/16/2007
- Molecular Biology:
- Alscript is a program for formatting sequence data for publication.
documentation example and demo files
- artemis genome browser. Java implementation.
Windows/Mac users should install it locally and run it that way.
manual
poster (overview)
From SAF server use: setenv display yourpc:0.0; gcgtogenbank.pl gcgfile genbankfile; art genbankfile .
- Cloneit is a tool for designing cloning experiments
- ClustalW (latest documentation is for 1.7, more recent version is installed)
- Clusters A set of locally written programs for analyzing the distribution of small motifs (tuples or "Nmers") in sequences.
Manual
- crimap Constructs multilocus linkage maps.
Manual
- darwin Sequence analysis package from the cbrg. Manuals
PDF
HTML
- dialign Multiple sequence alignment program. Manual
Text
- EMBASSY programs were originally separate
but have been integrated into EMBOSS. They use the same command line structure as all other
EMBOSS programs. They include:
- domainatrix for Protein Domain analysis
- domalign Protein Domain analysis
- domsearch for Protein Domain analysis
- emnu EMBOSS menu system
- esim4 Align an mRNA to a genomic DNA sequence
- hmmernew wrappers tfor the hmmer v2.3.2 programs
- iprscan wrapper for the interproscan program
- memenew wrapper applications providing an EMBOSS-style interface to the applications in the original MEME package version 4.0.0
- mira MIRA package is a fragment assembly program
- mse multiple sequence editor
- phylipnew EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69
- signature for Protein Domain analysis
- structure for Protein Domain analysis
- topo display membrane protein topology
- vienna VIENNA RNA package
- EMBOSS is a very large set of molecular biology programs that supplement and/or replace
GCG programs. Administration manual (PDF)
Program descriptions
- e-PCR Electronic PCR. Useful for locating STS markers in genomic DNA. documentation
command line arguments
- GCG is a very large set of commercial molecular biology programs (on old SPARC system only). Manual
- genefinder,Xgenefinder are used to locate (predict) exon/intron boundaries and list
the proteins which are predicted. Xgenefinder uses the X11 interface to display the
results graphically. Documentation
- Gibbs implements the GIBSS sampling strategy. (Version 3.1)
Manual
- HMMER Profile hidden Markov models for biological sequence analysis
2.3.2 manual ((version used in EMBOSS EHMMER* programs) PDF
- mapc,mapl,diged are programs by W. Pearson that calculate restriction maps
from double digests. Instructions
- nclever is a command line access to the NCBI's network Entrez service.Manual
- Paracel PGA assembly software (beta, limited availability)
Manual (PDF)
Release Notes
- paml paml phylogeny programs (regular command line versions) documentation
- pestfind Locates PEST sequences in plain text sequence files. No documentation.
Run from a command line and answer the prompts.
- PHYLIP Phylip 3.6a2 phylogeny programs (regular command line versions) descriptions
- phylo_win X11 based phylogenetic analysis program documentation
- Pise is a web interface to EMBOSS. A SAF username/password
is NOT required but data only remains on the server 24-48 hours. Be sure to use
an http (not https) URL or the icons won't load.
- r8s calculates divergence times from alignments. documentation.
Put together a file of commands and run it like:r8s -f commandfile
- saps Statistical Analysis of Proteins by Volker Brendel. man page
testpro file, result of: saps -s DROME testpro
without -d flag,
with -d flag
- sim4 program for aligning ESTs or mRNAs to genomic sequence documentation
- seaview X11 based multiple sequence editor documentation
- Staden package documentation
- W2H is a web interface to both GCG and EMBOSS. A SAF username/password
is required.
w2h start page.
- UW assembly programs:
Getting started,
GENERAL,
PHRED,
PHRAP,
PHD2FASTA,
SWAT
- Search all SAF documentation other than man pages
- Search all man pages
- Others:
- Molecular Biology:
- Alscript is a program for formatting sequence data for publication.
documentation example and demo files
- artemis genome browser. Java implementation.
Windows/Mac users should install it locally and run it that way.
manual
poster (overview)
From SAF server use: setenv display yourpc:0.0; gcgtogenbank.pl gcgfile genbankfile; art genbankfile .
- Cloneit is a tool for designing cloning experiments
- ClustalW
Version 2.0 program is clustalw2 documentation, version 1.83 program is clustalw.
documentation (for 1.7).
- crimap Constructs multilocus linkage maps.
Manual
- darwin Sequence analysis package from the cbrg. Manuals
PDF
HTML
- dialign Multiple sequence alignment program. Manual
Text
- EMBASSY programs were originally separate
but have been integrated into EMBOSS. They use the same command line structure as all other
EMBOSS programs. They include:
- domainatrix for Protein Domain analysis
- domalign Protein Domain analysis
- domsearch for Protein Domain analysis
- emnu EMBOSS menu system
- esim4 Align an mRNA to a genomic DNA sequence
- hmmernew wrappers tfor the hmmer v2.3.2 programs
- iprscan wrapper for the interproscan program
- memenew wrapper applications providing an EMBOSS-style interface to the applications in the original MEME package version 4.0.0
- mira MIRA package is a fragment assembly program
- mse multiple sequence editor
- phylipnew EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69
- signature for Protein Domain analysis
- structure for Protein Domain analysis
- topo display membrane protein topology
- vienna VIENNA RNA package
- EMBOSS is a very large set of molecular biology programs that supplement and/or replace
GCG programs. Administration manual (PDF)
Program descriptions
- e-PCR Electronic PCR. Useful for locating STS markers in genomic DNA. documentation
command line arguments
- GCG is a very large set of commercial molecular biology programs (on old SPARC system only). Manual
- genefinder,Xgenefinder are used to locate (predict) exon/intron boundaries and list
the proteins which are predicted. Xgenefinder uses the X11 interface to display the
results graphically. Documentation
- Gibbs implements the GIBSS sampling strategy. (Version 3.1)
Manual
- HMMER Profile hidden Markov models for biological sequence analysis
- mapc,mapl,diged are programs by W. Pearson that calculate restriction maps
from double digests. Instructions
- paml paml phylogeny programs (regular command line versions) documentation
- pestfind Locates PEST sequences in plain text sequence files. No documentation.
Run from a command line and answer the prompts.
- PHYLIP Phylip 3.6a2 phylogeny programs (regular command line versions) descriptions
- phylo_win X11 based phylogenetic analysis program documentation
- Pise is a web interface to EMBOSS. A SAF username/password
is NOT required but data only remains on the server 24-48 hours. Be sure to use
an http (not https) URL or the icons won't load.
- r8s calculates divergence times from alignments. documentation.
Put together a file of commands and run it like:r8s -f commandfile
- saps Statistical Analysis of Proteins by Volker Brendel. man page
testpro file, result of: saps -s DROME testpro
without -d flag,
with -d flag
- sim4 program for aligning ESTs or mRNAs to genomic sequence documentation
- seaview multiple sequence
editor, phylogenetic analysis. (X11 version) documentation. Native versions available.
- Staden package documentation
- W2H is a web interface to both GCG and EMBOSS. A SAF username/password
is required.
w2h start page.
- UW assembly programs:
Getting started,
GENERAL,
PHRED,
PHRAP,
PHD2FASTA,
SWAT
- Search all SAF documentation other than man pages
- Search all man pages
- Others:
WARNING - links below this point are not actively supported
- OpenVMS commands
- OpenVMS HELP
- OpenVMS Manuals
User's guides, programming language manuals, and so forth.
- OpenVMS CDE Manuals
Guides for the new desktop (not installed yet).
- OpenVMS HELP for some layered software
- OpenVMS programming
SAF notes, General information, E-mail
- Operating system information:
OpenVMS ,
POSIX ,
All
- Local system information:
SAF Notes,
General,
E-mail ,
All
- GCG (Help,
Manual,
WPI ),
EGCG ( Help,
Manual),
Phylip,
All
- All other manuals