Jigyasa Arora

Using different starting NCBI taxonomy gives different results

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Hey @shenwei356 and @nick-youngblut Thank you so much for writing the python scripts to convert taxonomy between NCBI and GTDB. It will save so much time as compared to redoing...

Hey all! I am using the default settings of phytime on my dataset. My dataset is in the same format as the example dataset, but phytime is not running at...

Hey all! I have a slightly technical question. The examples in the manual show that a) we can have different rates (R1,R2,R3,R4,R5 etc.), b) which can have different init.values (eg....

phytime not working on the dating_example.xml

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Hey! I am testing the phytime run on the example file, and I get the following error- code- `phytime --xml=dating_example.xml` error- ` . 1365 patterns found (out of a total...

Hey All I am trying to install the github version of blobtools and running into the following error. Please find the code to reproduce the error. `module load python/3.7.3` `module...

taxify "IndexError: list index out of range"

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Hey All I am taxify-ing the blast output file against Uniprot database, following the tutorial here- https://blobtools.readme.io/docs/taxid-mapping-file. The accessions file looks like this- A4YCM6 NCBI_TaxID 399549 A4YCM7 NCBI_TaxID 399549 A4YCM8...

merge step required for analyzing the R1 reads only?

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Hi @benjjneb , I am analyzing the R1 reads only for 16S data and I wanted to confirm if the merge step is still required for this? In the tutorials,...

Is it possible to get labels info from the dendrogram object?

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Hey! Thank you for the interesting package! I am interested coloring the branches of a dendrogram. I am able to do so with the set() functions, but the colors are...

Does DEICODE meet the assumption of same "multivariate spread" among groups for PERMANOVA?

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Hey @gregcaporaso I wanted to ask if all DEICODE transformed data meet the main assumption for PERMANOVA? [https://stackoverflow.com/questions/35410860/permanova-multivariate-spread-among-groups-is-not-similar-to-variance-homogeneit] I tested it on my data after DEICODE transformation. Only some datasets...

collapse the deicode distance matrix back into feature tables before rpca function?

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Is it possible to condense (or collapse) the deicode distance-matrix back into features but keeping the log-ratio transformations and matrix-filling? As for any of the downstream phylogenetic analysis, the functions...