**1.7k**wrote:

I tried to run RaxML(https://sco.h-its.org/exelixis/resource/download/NewManual.pdf) tool to generate phylogenetic tree (Maximum Likelihood tree) using the command below. I ran 100 bootstraps and got the tree, but the bootstrap value on the tree is 100 for all branches. I compared the same data and made the ML tree with mega which gave me similar topology but completely different bootstrap values. Could someone please help me if there is anything I am doing wrong with my commands below. Thanks for your help in advance.

Here is my aligned fasta file: https://www.dropbox.com/s/9s05msdpn67tqnh/test_mpk.fas?dl=0

Performed model test using PROTGAMMAAUTO command:

`raxmlHPC-PTHREADS -s test_mpk.fas -n mpktreeml -m PROTGAMMAAUTO -p 84381764921 -T 20`

Then, I ran 100 boostrap trees:

`raxmlHPC-PTHREADS -s test_mpk.fas -n mpktreeml_bootstrap_r -N 100 -m PROTGAMMAJTT -p 427482396541 -T 20`

concatenated all tree files:
`cat mpktreeml_bootstrap_r* > allBootstraps`

Tested majority rule consensus:

`raxmlHPC-PTHREADS -z allBootstraps -m PROTGAMMAJTT -I autoMRE -n TEST -p 3824142315 -T 20`

Then finally, got the tree:

`raxmlHPC-PTHREADS -f b -z allBootstraps -t mpktreeml_bootstrap -m PROTGAMMAJTT -n mpkBOOTSTRAP.txt`

I then used itol to view mpkBOOTSTRAP.txt which looks like this: https://www.dropbox.com/s/gi6i6vkisu8eue4/0FklaRAXqssnABHmZR-Cow.pdf?dl=0

The tree above looks good except it doesn't show correct bootstrap values compared to the tree generated by mega: https://www.dropbox.com/s/xy06glvud0izr1q/mega_mpk_tree.pdf?dl=0