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The goal of the basic workflow is to be able to consume unaligned FASTA, align this (i.e. solve #3) and build a tree with it (by addressing #4). These steps are implemented with tools, scripts, and we…
rvosa updated
4 years ago
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Hi, thanks for the great repo. I'm interested in generating sequences with bmDCA for protein families that have around ~20k samples with ~400-600 total aligned positions (and no position with more tha…
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Some of the unit tests produce warnings like the following:
```
test_bad_fancy_index (skbio.alignment.tests.test_tabular_msa.TestLoc) ... /Users/jonsanders/Development/git_sw/scikit-bio/skbio/alig…
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I made multifasta files of genes of interest of several genomes and used them as input files in a directory called genomes as following
singularity exec /apps/singularity-images/metachip_1.10.2.sif M…
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Hi
I've used your code to mask recombination regions in MSA, and it works really well (thank you!). However, I am currently working with a gene alignment which is in xmfa format. CFML has given me th…
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Dear Diego,
I am running modeltest on a big protein MSA (~300,000 sites, 1344 species, ~1000 partitions) on supermuc.
I managed to treat one third of the partitions on 20 nodes within the wall t…
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We need an option in the find_last_approve_ELIG_version that does not use the code 99 on the command line.
This has only been found in MSA so the functionality is specific to MSA at this point.
…
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Hi
Few days ago, I downloaded the MetaCHIP(V1.10.9) and succeeded in testing the example data. But when I run MetaCHIP with the data myself, the error occur below:
command: MetaCHIP PI -p…
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Assalamu aleykum.
I can not find reference information in API request. How can i get the reference information of Hadith via API?
Example the below information.
Reference: Sahih al-Bukhari…
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For all experiments, we will have (unless mentioned otherwise):
- number of MSA sites = 1000 * (number of displayed trees)
- perfect sampling: sites are sampled proportionally to the displayed tree …