Hi Niranjan,

Could you please explain the parameters you have selected in RAxML in Cipres portal. Whether you uploaded any partition file. option-- Use a mixed/partitioned model (-q)

Best

Vineesh

I used the RAxML-HPC2 on XSEDE model,

Estimate proportion of invariable sites (GTRGAMMA + I)

Regards,

Niranjan

If you are using mutiple genes, better to use a partition model. you can generate it using ModelFinder.

Maximum Hours to Run (click here for help setting this correctly) * 1 hr/2hr -depends on your data size

How many patterns in your data set?( total length)

Specify the number of distinct rate categories (-c) *-give any number- i gave 25

Specify a random seed value for parsimony inferences (-p) * select this one

Use a mixed/partitioned model? (-q) -If you know

Specify an ML estimate of base frequencies (GTRGAMMA + X) no

Estimate proportion of invariable sites (GTRGAMMA + I) no

Choose model for bootstrapping phase + GTRCAT

Evaluate DNA partitions only under this model [Not Mandatory] (if you are uploading partition file) or you can select any other option.

Select the Analysis Type * Rapid bootstrap analysis / search for best-scoring ML tree (-f a)

Choose a Bootstrapping Type Rapid Bootstrapping (-x)

Specify bootstrap protocol + Specify an explicit number of bootstraps.

try this one and let me know

Thank you Vineesh for the valuable information.

The multigene data set patterns 4603