Carlos Peña carlosp420
carlosp420
/ remove_rates.sh
Last active
October 12, 2015 04:08
remove rate parameter of trees from BEAST runs
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| egrep '\[?\&?\w+\.rate=[0-9]{1,3}\.[0-9]{1,20}E?-?[0-9]{0,4},?\]?' | |
| sed -e 's/\[\?&\?\w\+\.\w\+\.\?rate=[0-9]\{1,3\}\.[0-9]\{1,20\}E\?-\?[0-9]\{0,4\},\?\]\?//g' tree_file.tree > slim_tree_file.tree | |
| sed -r 's/\[?&?\w+\.rate=[0-9]{1,3}\.[0-9]{1,20}E?-?[0-9]{0,4},?\]?//g' |
carlosp420
/ sort_by_tip.label
Created
October 8, 2012 11:36
R: sort a data.frame of taxon names according to tip labels of phylogeny
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| tax <- read.csv("richness.csv"); # col.names => "exemplar", "n.tax", "taxon" | |
| tax[match(phy$tip.label, tax$exemplar),] |
NewerOlder