Nabil-Fareed Alikhan comments

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                                            Nabil-Fareed Alikhan

How to make phylogenetic using binary data

Grapetree isnt really designed for this data. you can make a tree from binary data in something like IQTREE. http://www.iqtree.org/doc/Tutorial#binary-morphological-and-snp-data and then visualize the resulting tree file with grapetree.

Investigate the effects of using hsp.identities/float(record.query_length) >= tol vs max_identity >= tol

I use the following in Dryad to allow users to specify a minimum % identity over a minimum % of gene length. (where lenCutOff is the percentage of original gene...

BRIG keeps generating SYS_ERROR:org.xml.sax.SAXException: value for 'sequenceLength' attribute in cgview element must be less than 20000000 in null at line 1 column

Hi. Your reference is huge. Over 20MB. On Mon, 9 Dec 2019, 10:52 com31, wrote: > [image: Screenshot from 2019-12-09 16-20-04] > > Can anyone helped me with this issus...

Multifasta is broken. Query or input gives no rings.

hi @happykhan - ive been using CGview tools and notice that the file extension for reference genome needs to be .fasta and the comparison genomes needs to be .fna

Multifasta is broken. Query or input gives no rings.

Wait, why am i talking to myself?