Hi All,
I developed ML tree using Treemix. Then uploaded treemix output file (mltree.treeout) into FigTree to draw the tree.
I ran this step "treemix -i input file.gz -bootstrap -k 500 -o replicate1 I did bootstap" in Treemix to get the bootstrap values and got the output (replicate1.treeout )file.
When I upload two files I get totally different trees. I do not know how to get the bootstrap values into my ML tree.
If someone could assist me, I would be grateful.
Thanks :)
Hi Buddhika, you should now combine your best ML tree with the pseudoreplicate trees in a single tree file. Try the bipartitions function in RAxML freely available in the CIPRES website or in your computer. Hope this helps.
Hi Bruno F Melo,
Thanks for your kind reply. Last couple of days I was working on RAxML as you suggested. Still could not figure it out. I tried using RAxML GUI 2.0, as it says it is a graphical user interface to RAxML. However, it does not recognize my output files from Treemix. My dataset is a binary haploid dataset, thus it limits us using many software developed for phylogenetic analyses such as migration and ML tree. Thank you :)
Buddhika
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