Seq-Gen
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rambaut
Sequence simulator
currently, only HKY, F84 & GTR are for nucleotides. @rambaut
For example: [300, 0.5](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4); [400, 1.75](((Taxon1:0.2,Taxon3:0.2):0.1,Taxon2:0.3):0.1,Taxon4:0.4); [300, 0.75](((Taxon1:0.2,Taxon2:0.2):0.1,Taxon3:0.3):0.1,Taxon4:0.4); how to know the rate is 0.5, 1.75, and 0.75 for the three trees?
When I tried to compile this the executable file was created in the source directory, not its parent with the README as suggested
There is a small bug where the order of the branches: - in the ancestral output branch 0,1,2 https://github.com/rambaut/Seq-Gen/blob/e8660d73769297d25a88b40d5b828a6fce7784b5/source/evolve.c#L569 - while in the WriteTree the order was 1,2,0 https://github.com/rambaut/Seq-Gen/blob/e8660d73769297d25a88b40d5b828a6fce7784b5/source/treefile.c#L567 This...
Hi, We have this project as a package in Debian currently Whilst I agree that every file containing "code" has a BSD license on top of it, but due to...
Similar to #9 but I can't solve it with regex. I downloaded the nextstrain tree (Jan 4, 2021) for nCov and wanted to run TreeToReads.py with it (newick attached below)....
Hello, what is the [license](https://help.github.com/articles/adding-a-license-to-a-repository/) for this repository?
For long time seq-gen was considered non-free due to non-free license of paml parts. Currently the situation has changed and paml is released under GPL license. I wonder if you...
It is not possible to echo a string into `seq-gen` to use as a tree: ``` $ echo "(A:0.1,B:0.1,C:0.1);" | /home/sam/ware/Seq-Gen.v1.3.3/source/seq-gen -mGTR Sequence Generator - seq-gen Version 1.3.2x (c) Copyright,...
