Sequence feature loci site analysis toolkit
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ClustalOmega
ClusterMatrix
DNA_Comparative
MSA
MotifScanner
NeedlemanWunsch
Pfam-HMM
SNP
SequencePatterns.Abstract
SequencePatterns
SequenceTools
SmithWaterman
data
etc/SequenceLogo
.gitattributes
.gitignore
1-11bp.NT_seeds.rar
5207004.pptx
LICENSE
README.md
SNP.sln
SequenceTools.sln
algorithms.sln
creates_logo.png
seqtools.md

README.md

GCModeller Sequence Utility Tools

Pfam-hmm

Hidden Markov Model for Pfam-A

HMM data can be download from EMBL ftp website:

ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam29.0

Sequence repeats

Drawing the sequence logo

1.Multiple alignment

Multiple align of the sequence, this can be applied by the clustal program

2.Draw logo

Using /logo command from the seequence CLI tools to draw the sequence logo from the multiple sequence alignment result

G:\4.15\MEME\footprints>seqtools ? /logo

Help for command '/logo':

  Information:
  Usage:        F:\GCModeller\GCModeller-x64\seqtools.exe /logo /in <clustal.fasta> [/out <out.png>]
  Example:      seqtools /logo