The program gotree could be used to write into $outtree the strict consensus tree (Sokal and Rohlf 1981) of the forest contained in the NEWICK-formatted input file $intrees.
Of note, when the input trees have branch lengths, the length of each branch of the strict consensus tree is the average length of the same branch over all the input trees containing it. However, the following command line could be used to discard every branch length:
The following command lines allows writing into $outtree the majority-rule consensus tree (with frequencies as branch supports; Margush and McMorris 1981) of the forest contained in the NEWICK-formatted input file $intrees.
The program IQ-TREE could be used for inferring a majority-rule consensus tree with the following command lines:
iqtree -con -t $intrees -minsup 0.5 -pre $outtree && mv $outtree.contree $outtree && rm $outtree.log The program gotree could be used for inferring a majority-rule consensus tree with the following command lines:
Of note, when the input trees have branch lengths, the length of each branch of the consensus tree is the average length of the same branch over all the input trees containing it. However, the following command line could be used to discard every branch length:
The extended majority-rule consensus tree is also called the greedy consensus tree (see Bryant 2003). The program IQ-TREE could be used to write into $outtree an extended majority-rule consensus tree (with frequencies as branch supports) of the forest contained in the NEWICK-formatted input file $intrees.