Issues with input species tree formatting

[Riyad Hossen]

Hi, I am new in coding and simulation work. I was trying to simulates 675 gene trees using my binary ultrametric time calibrated species tree as guide template. But SimPhy gave me an error massage that related with input species tree. I tried many ways to solve and the error massage is consistent. I understood that is for lack my background knowledge on coding or file formatting. Expecting help from you guys.

****the species tree I used in newick format ---

(((nmr:238.3809742,(actbcl:119.1183601,actbkl:119.1183601):119.2626141):238.2594125,(chlrer:238.3373693,(chlrsr:119.1665366,polclv:119.1665366):119.1708327):238.3030175):238.3596132,((............,halopn:5.033481982,halmn:5.033481982):7.09557094):3.124460354):15.64807366):3.732030647):20.37671079):11.85601912):66.95428576):45.30177979):178.3580994):119.1945577):238.3249298);

***The error massage is --

ERROR: There is something wrong in the tree
 <- HERE
        Tree is not finished with ;
        There are a defect of nodes related with the number of branches. Maybe there are a missed comma, or the root node have branch length (it must not have it)

Settings error: : Error in the Newick species tree

Riyad

[Riyad Hossen]

This species trees  I tried as input, and found the same error massage.

[Diego Mallo]

Dear Riyad,

I suspect you are trying to input the Newick tree file using SimPhy’s -s option; however, that option expects the actual tree string as an argument in the command line (e.g., simphy -s "((A:100,B:100):50,D:150);”) instead of a tree file. You can use the -sr option to input a tree file, but the tree file must be formatted in Nexus. 

I am attaching the same tree formatted in Nexus, which works well for me (e.g., simphy -sr species_time_tree.nex -ld f:0.0000005 -lb f:0.0000005 -lt f:0.0000005 -rl U:10,100 -rg 1 -o SimPhy_test -sp f:10000 -su f:0.00001 -sg f:1 -om 1 -v 2 -od 1 -op 1 -oc 1 -on 1 )

Let me know if you are still having issues.

DM