2010-01-02 19:00:27| 分类: Bioinformatics | 标签: |举报 |字号大中小 订阅
COMMON FILE CONVERSION ATTRIBUTES
The default input formats are determined by a file’s extension (e.g., a file with the extension of ".ig" is initially assumed to be in "IG" input format).However, you have the option to specify any format for any file; the file extension is simply used as an initial guide. Note that the specification of an incorrect file format most often results in an erroneous conversion or other unexpected error.
CLUSTAL Format
The sequence alignment outputs from CLUSTAL software often are given the default extension .aln. CLUSTAL is an interleaved format. In a page-wide arrangement the sequence name is in the first column and a part of the sequence’s da
The CLUSTAL file above would be converted by MEGA into the following format:
MEGA Format
For MEGA to read and interpret your da
Alignment format
When working in MEGA’s Alignment Explorer you can choose to save the current state of all da
TreeView Document format
TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs. TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the da
FASTA format
A sequence in FASTA format begins with a single-line description, followed by lines of sequence da
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRTQIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWCHFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCKMDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKKTYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGFAPTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNLLAAVEAQQQMLKLTIWGV
The FASTA file format is very simple and is quite similar to the MEGA file format.
PHYLIP (interleaved) Format
The PHYLIP format is interleaved, similar to the MSF format. It consists of a line of numeric da
MEGA would convert this da
References:
http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
The help file of MEGA 4.1 (Beta 3 )
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
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