Mercurial > repos > boris > phylorelatives
changeset 32:034181b4b1b8 draft
Uploaded
| author | boris |
|---|---|
| date | Mon, 10 Jun 2013 00:43:49 -0400 |
| parents | 75dcc9910f6d |
| children | 8d663949bdc8 |
| files | phylorelatives.xml |
| diffstat | 1 files changed, 14 insertions(+), 11 deletions(-) [+] |
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--- a/phylorelatives.xml Mon Jun 10 00:43:11 2013 -0400 +++ b/phylorelatives.xml Mon Jun 10 00:43:49 2013 -0400 @@ -44,7 +44,7 @@ <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" /> <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/> <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick"/> - <data format="png" name="plot" label="${tool.name} on ${on_string}: plot"/> + <data format="txt" name="plot" label="${tool.name} on ${on_string}: ascii plot"/> </outputs> <tests> <test> @@ -58,10 +58,6 @@ - -(boris-at-bx.psu.edu) - - ----- .. class:: infomark @@ -70,7 +66,7 @@ Constructs relatedness of a set of sequences based on the pairwise proportion of different sites. One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor). -It returns the FASTA multiple alignment used, and reports a table with the relatives of the minor allele sequence in a NJ tree, the tree plot and newick string. +It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives per minor allele sequence, the tree plot and newick string of the tree. ----- @@ -79,8 +75,7 @@ **Note** This tools DOES NOT align the sequences. -The FASTA multiple alignment file is fabricated by concatenating same length homologous sequences. -An independently aligned FASTA multiple alignment file can be used as well. +Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation if more than one FASTA file is provided. ----- @@ -88,9 +83,9 @@ **About formats** -**FASTA multiple alignment** -- +*FASTA multiple alignment* -describe format shortly +See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format ----- @@ -104,10 +99,18 @@ >sample4_major -- running this tool with **b = 1000** **m = yes** **root = RSRS**, will return:: +- running this tool with *b = 1000* *m = yes* *root = RSRS*, will return:: newick relatives plot + +----- + +**Citation** + +If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.* +(boris-at-bx.psu.edu) + </help> </tool> \ No newline at end of file