tag:blogger.com,1999:blog-3342041114052632712.post8698807834355895316..comments2024-01-20T16:39:42.179+11:00Comments on PhyloBotanist: Species trees from SNPs with SVD quartetsAlex SLhttp://www.blogger.com/profile/00801894164903608204noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-3342041114052632712.post-74686491968706902542017-11-08T21:27:17.898+11:002017-11-08T21:27:17.898+11:00I just ran a quick SVD analysis on 4a158 and get t...I just ran a quick SVD analysis on 4a158 and get the bootstrap values on the resulting tree using your savetrees command, only they appear to be saved as branch lengths. Have you tried adding the parameter savebootp=nodelabels?Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-3342041114052632712.post-57921926787164506242017-11-08T17:31:17.331+11:002017-11-08T17:31:17.331+11:00Great post. I just ran svd quartet analysis with P...Great post. I just ran svd quartet analysis with PAUP like you did in linux. However, the final tree does not have bootstrap values with it.<br /><br />this is my command line at the end of the nexus file. Did you have this issue?<br /><br />begin paup;<br /> log file=svd.txt;<br /> lset nthreads=3;<br /> SVDQuartets evalQuartets=random speciesTree=yes partition=gabriel_data bootstrap=standard nreps=10000 ambigs=distribute treeFile=svd.tre;<br /> savetrees file=svd_boot.tre from=1 to=1 maxdecimals=2;<br /> log stop;<br /> quit;<br />end;<br /><br />gdvalehttps://www.blogger.com/profile/10724510767610610006noreply@blogger.com