NEWICK-formatted tree transformation

Let $tipfile be a text file containing one or several leaf name(s) to discard from the phylogenetic tree contained in the NEWICK-formatted file $treefile (with or without branch lengths and/or supports). The program gotree could be used to discard the specified leaf name(s) and write the resulting subtree into the NEWICK file $outtree with the following command line:

gotree prune -i $treefile -f $tipfile -o $outtree 

Alternatively, a similar command line could be used to discard leaves that are absent from an other phylogenetic tree contained in the NEWICK-formatted file $alttree:

gotree prune -i $intree -c $alttree -o $outtree

The following command lines allow collapsing branch(es) of length lower than a specified value $cutoff within the tree contained in the NEWICK-formatted file $treefile and writes the resulting tree into the NEWICK file $outtree.

gotree

The program gotree could be used to collapse short branch(es) with the following command line:

gotree collapse length -i $treefile -l $cutoff -o $outfile

awk

The following awk one-liner allows collapsing short branch(es):

awk -v bl=$cutoff '{l=length(t=t$0)} END{--l;x=1;while(++x<l){if((c=substr(t,x,1))=="("){p[++i]=x;continue}if(c==")"){y=x;while(substr(t,++y,1)!=":"){}z=++y;while((c=substr(t,++z,1))!=","&&c!=")"){}(substr(t,y,z-y)<bl)&&(l=length((t=substr(t,1,(op=p[i])-1)substr(t,++op,(x-=2)-op+2)substr(t,z)))-1);--i}} print t}' $treefile > $outfile

The program gotree could be used to collapse the branch(es) with support lower than a specified value $cutoff. The following command line allows collapsing such branch(es) within the tree contained in the NEWICK-formatted file $treefile and writes the resulting tree into the NEWICK file $outtree:

gotree collapse support -i $treefile -s $cutoff -o $outfile

The following command lines allows discarding every branch length from the NEWICK-formatted tree file $treefile. The resulting tree is written into the NEWICK file $outtree.

gotree

The program gotree could be used with the following command line:

gotree clear lengths -i $treefile -o $outtree

sed

The following sed one-liner discards every branch length from the input tree file:

sed 's/:[0-9\.-]*//g' $treefile > $outtree

The following command lines allows discarding every branch support from the NEWICK-formatted tree file $treefile. The resulting tree is written into the NEWICK file $outtree.

gotree

The program gotree could be used with the following command line:

gotree clear supports -i $treefile -o $outtree

sed

The following sed one-liner discards every branch support from the input tree file:

sed 's/)[0-9\.-]*/)/g' $treefile > $outtree

The following command lines allows discarding every branch length and support from the NEWICK-formatted tree file $treefile. The resulting tree is written into the NEWICK file $outtree.

gotree

The program gotree could be used with the following command line:

gotree clear lengths -i $treefile | gotree clear supports -o $outtree

Shell

The following command line based on sed discards branch lengths and supports from the input tree file:

sed 's/:[0-9\.-]*//g' $treefile | sed 's/)[0-9\.-]*/)/g' > $outtree

Let $mapfile be a text file containing, for each line, a taxon name to be renamed by a new taxon name, both being separated by at least one blank space. The following command lines allows performing this renaming within the tree contained in the NEWICK-formatted file $treefile. The resulting tree is written into the NEWICK file $outtree.

gotree

The program gotree could be used with the following command line:

gotree rename -i $treefile -m $mapfile -o $outtree

awk

The following awk one-liner leads to the same result:

awk 'NR==FNR{m[$1]=$2;next} {t=t$0}
     END{for(s in m){sub("\\("s",","(;"m[s]";,",t);sub(","s",",",;"m[s]";,",t);
                     sub("\\("s":","(;"m[s]";:",t);sub(","s":",",;"m[s]";:",t);
                     sub(","s")",",;"m[s]";)",t)}  gsub(";","",t); print t";"}' $mapfile $treefile > $outtree

The following command lines allows multiplying by the factor $scale every branch length of the tree contained in the NEWICK-formatted file $treefile. The resulting tree is written into the NEWICK file $outtree.

gotree

The program gotree could be used with the following command line:

gotree brlen scale -f $scale -i $treefile -o $outfile

awk

The following awk one-liner rescales the branch lengths of a phylogenetic tree ($prec is the number of decimal places):

awk -v s=$scale -v p=$prec '{t=t$0} END{while((c=substr(t,++x,1))!=";")if(c==":"){y=++x;while((c=substr(t,++y,1))!=","&&c!=")"){}t=substr(t,1,x-1)sprintf("%."p"f",s*substr(t,x,y-x))substr(t,y)} print t}' $treefile > $outfile