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Prepare the language distances based on:
* mutual coverage best subset
* selected taxa (see below)
* phylip format
* compute cognates based on phenetic algorithm (SCA) with threshold 0.45 (or mayb…
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Hello!
My name is Andrea and I am bioinformatician from Spain. I have been using tn93 for a while, including it in some of the pipelines I am developing in order to analyze HIV sequences more effecti…
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Hi,
This looks super-cool, but do you plan to publish any instructions on how to use it also? :)
Another small question. You state in your paper for PROTAX-GPU that...
> [...] before computing …
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# Overview
In the Fall of 2023, I moved over a bunch of stuff from PowerPoint slides (nearly) verbatim. I was in a rush, so I told myself to move it just move it over and improve it later.
Go ba…
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What is the output supposed to look like?
I have a bcf.gz file that I ran hoping to calculate distances between 347 individuals. I do not think the documentation is super clear, so I ran it like th…
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## The problem
TreeTime has currently a very rudimentary way of resolving polytomies (multi-furcations in the tree).
When this was initially put in place it was never meant to resolve large polyt…
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Hi,
I am following this protocol: https://www.nature.com/articles/nprot.2010.116. At some point it will make use of `smartpca`. This works beautifully for HapMap 3 data:
```
perl ~/git/EIG/bin/…
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I have few queries after analyzing my output:
1. The travel time of agents in output plan file, from Selected Plan = "yes", is different than legs.csv or trips.csv in the output folder. The travel di…
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Hello,
I want to run smartpca using .ped and .map files.
Prior to running the code, I had to change 2 things in the .map file
1) Replace 0's in Chromosome column with 40
2) Since it compl…
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As I mentioned, Tim Doyle (Florida DOH) finally sent his data. He has exported a subset of genetic links from his overall dataset, and has a very simple file with Source, Target, distance info. I trie…