harvest

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Hi. When i create a snapshot for tree and alignment in png or jpeg format and save it in the desktop, the file doesn’t exist and not appear. Until the...

Ivalize

majority of input genomes get ignored

3

Hi, I ran parsnp in the fasta-reference mode only (so no genbank file). I put more than 500 query genomes into a folder, but only 36 of them were actually...

karchern

Hello, I have been having an issue while running parsnp. Sometimes parsnp only includes a very limited number samples in the sample_directory. It normally is under 10 samples. **I run...

ghost

Question about Gingr

3

 I met a problem when using gingr on cluster. The name of genome can not be shown in the phylo tree. They are all black blocks. I would like...

gsong1205

Hi, Sorry for the stupid question but I couldn't find an answer. As said in the title, for the following parameter : **-a = : min (a)NCHOR length (default =...

ghost

Hi, I am looking for insertion and deletion in my dataset with Parsnp and Harvesttools. I have SNP information in VCF output file but no indels information. My command is:...

XueqiongLi

What is the different between Newick formatted core genome SNP tree and the tree in Gingr file

1

tangna2017

alignment of 1000 Klebsiella pneumoniae genomes with parsnp

5

Hi Treangen, Thank you very much for the software. I have no difficulties in genomes alignment of a small sample sizes (up to 45 bacterial genomes). But I am faced...

itsvetkova

need some help with -c

1

thanks for the programme which really helps our work!!! I've come across a few problems and have a few questions :) 1. in a folder I've got 24 fasta, but...

fengyuchengdu

Hi, When I run parSNP on 14 genomes with a random reference genome, the output file only includes 12 of them. I am using parSNP with the -c command. I...

jlf292