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lliu1871 / mp-est

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function
GNU General Public License v3.0
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mp-est 2.1 couldn't analysis more than 100 species #3

Open zhangzhiyangcs opened 2 years ago

zhangzhiyangcs commented 2 years ago

Hi Liang, I have gene trees consisted by 106 species. When I run the mp-est v2.1, the segment fault occured. I applied mp-est v2.0 using the same control file and gene tree files without error. Besides, I have another question that mp-est required the root binary gene tree. There are some tree didn't meet this requirment. While astral software didn't report this issue, I want to compare the results of two softwares with the same input data sets.
Best wishes, Zhiyang

lliu1871 commented 2 years ago

Hi Zhiyang,

The input of astral are unrooted gene trees. It does not require gene trees to be rooted. Could you send me the gene trees of 106 species? I will fix the problem.

Liang

Liang Liu Graduate Coordinator Department of Statistics Institute of Bioinformatics University of Georgia Phylogenetics Lab | Phylogenetics Lab (uga.edu)http://faculty.franklin.uga.edu/lliu/ @.***

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Hi Liang, I have gene trees consisted by 106 species. When I run the mp-est v2.1, the segment fault occured. I applied mp-est v2.0 using the same control file and gene tree files without error. Besides, I have another question that mp-est required the root binary gene tree. There are some tree didn't meet this requirment. While astral software didn't report this issue, I want to compare the results of two softwares with the same input data sets. Best wishes, Zhiyang

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zhangzhiyangcs commented 2 years ago

mp-est_test_data.zip There are results from mp-est v2.0. The gene trees of 106 species is named gene_tree ( compelety the root binary gene tree) and gene_tree1. Thanks a lot.