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Update README
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yinlabniu authored Sep 25, 2019
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Expand Up @@ -79,7 +79,7 @@ supplied by this package, though if you are dealing with a query or
subject that isn't on our tree, you may have to add it in manually
into our own trees. We provide the names and nodes files downloaded
from NCBI (ftp.ncbi.nih.gov:/pub/taxonomy) which are available at
cys.bios.niu.edu/HGTFinder:
bcb.unl.edu/HGTFinder:
names.dmp: A file delimited by "[tab]|[tab]" where the first
column is the tax id and the second is the name of the genome.
the third column is a descriptor, it's unused by HGTFinder
Expand All @@ -95,7 +95,7 @@ database, you'll need to use our included DBFormatter tool to
format your database. The input file for this DBFormatter tool is
simply a multi-lined file where each line has a protein ID (from
the database) and a taxonomic ID associated with the protein ID. We
provide an example of such a file, available at cys.bios.niu.edu/HGTFinder:
provide an example of such a file, available at bcb.unl.edu/HGTFinder:
nr.tax

If you decide to use your own custom database, you'll be required
Expand Down Expand Up @@ -277,7 +277,7 @@ information while the program is running. You can mute this using
7 | Example Run
****|*****************

The Sample_Test folder is available for download at cys.bios.niu.edu/HGTFinder
The Sample_Test folder is available for download at bcb.unl.edu/HGTFinder

To run the sample test from the terminal, run:
./HGTFinder -d Sample_Test/Aspfl1.blast.out -s Sample_Test/Aspfl1.blast.self -t 332952 -o Sample_Test/TestOut/HGTOut -r 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9
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