User: tiagoantao

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tiagoantao660
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United States of America
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http://tiago.org/
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tiagoantao
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Last seen:
1 year, 9 months ago
Joined:
7 years, 11 months ago
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Posts by tiagoantao

<prev • 55 results • page 2 of 6 • next >
3
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Answer: A: LOSITAN failing during run - anyone able to help?
... Lositan is an old program and becomes more problematic with each new version of Java (It is JVM based implemented in Jython). I am currently not planning to release a new version soon. If the Force mean FST is not working there is an alternative: Run with the dataset FST If the realized FST is ...
written 4.1 years ago by tiagoantao660
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Job: Job: Researcher in Bioinformatics, Tropical Medicine, Portugal
... Dear all,   There is a Bionformatics position with a salary at a lecturer/assistant professor level, for 3 years in the Institute of Tropical Medicine in Lisbon, Portugal.   For more details please check the website ...
jobs written 4.2 years ago by tiagoantao660
10
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Answer: A: ipython notebooks on bioinformatics and genomics
... I have developed quite a few: A ongoing conversion of the Biopython tutorial A set of notebooks for population genetics simulation The notebooks from my book Bioinformatics with Python Cookbook In terms of scope, the ones related to the book cover a lot of areas. ...
written 4.8 years ago by tiagoantao660
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Comment: C: Lositan freezing when producing selection table
... Can you send me your input file (to my email address)? I need to have a look at that. ...
written 5.0 years ago by tiagoantao660
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Answer: A: Lositan; spiky confidence interval, too many outliers
... This is, I am afraid due to sampling effects related to the number of populations, there are two alternatives here: 1. You think that you have 2 populations overall (i.e. you sampled 2 out of 2 in the wild), and in this case the CI that Lositan is computing is not trustable 2. You think that you h ...
written 5.2 years ago by tiagoantao660
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Answer: A: Lositan; spiky confidence interval, too many outliers
... Sorry for the late answer. There is something that is not clear to me at this stage: What value is lositan reporting for the sample size (is that 10?). This is different from the total number of simulated populations (which would start as 2 in your case). If I understand well, you have 76 samples. ...
written 5.2 years ago by tiagoantao660
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Comment: C: Lositan; spiky confidence interval, too many outliers
... Just to be sure: on the bottom middle panel you have: Mean Fst Expected total pops Mutation Model Sample size. Are you reporting the "Expected total pops" or the "sample size"? ...
written 5.2 years ago by tiagoantao660
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Comment: C: Lositan; spiky confidence interval, too many outliers
... So, are you splitting this in two populations? or more? What is the sample size reported when you load the data? ...
written 5.2 years ago by tiagoantao660
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Comment: C: How to reduce the number of SNPs for the Lositan software
... Hi, You are using the large marker version right? http://www.popgen.net/soft/lositan/3264.html What is your operating system? Could you please start the Java console and post the error here? If I remember well the limit is 100,000 (less on Mac, like 40,000). If you randomly trim the genepop fi ...
written 5.5 years ago by tiagoantao660
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Answer: A: Why is LOSITAN not running the simulations?
... This is really a strange error and I have never seen this, for now I would recommend trying to run this on another PC and see if the problem repeats... ...
written 5.5 years ago by tiagoantao660

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