User: NickJD

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NickJD0
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Posts by NickJD

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Comment: C: ClustalO .phylip output is Broken?
... Thank you for this. I found that if I get ClustalO to output in FASTA format for the MAS, FASTTREE and other software understands it and I can still get the trees to build. What use are standards if we do not keep to them? ...
written 5 months ago by NickJD0
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Comment: C: ClustalO .phylip output is Broken?
... I am sure it is a problem with how ClustalO formats its Phylip output. ClustalW produces the same correct output as ClustalX ...
written 5 months ago by NickJD0
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Comment: C: ClustalO .phylip output is Broken?
... Yes you fixed it. Thank you. I used the newest version listed here for Linux: http://www.clustal.org/omega/ 1.2.4 I also used the version from apt install clustalo which is listed at 1.2.4 I think the ID spacing is indeed down to length, I can shorten my ID lengths to fix that. It does seem to be ...
written 5 months ago by NickJD0
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Comment: C: ClustalO .phylip output is Broken?
... Hi, I have checked the input and the output. I know this seems silly to think the output would be different but it is. The output snippets I uploaded are from the final line of the seq IDs. As you can see, the universal different is that there is no gap between the ID and then '---' in ClustalO a ...
written 5 months ago by NickJD0 • updated 5 months ago by Joe18k
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ClustalO .phylip output is Broken?
... Hi, I am trying to produce a .phylip file output using the ClustalO/X systems. I have a test set of 7 viral genomes (30kb) and I have run them through both the default options of ClustalO and ClustalX. The ClustalX software seems to produce a phylip file which works with other software such as Fas ...
clustalo multiplealignment clustal phylip written 5 months ago by NickJD0 • updated 5 months ago by h.mon31k
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EggNOG classes - What are they? e.g. bacNOG vs bactNOG
... There are many different COG classes. This page here lists many but without explanation and I can not find any definition for the classes anywhere: http://eggnog5.embl.de/download/eggnog_4.5/data/ Is this a known problem? ...
eggnog cog nog functional class written 6 months ago by NickJD0
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Comment: C: Ensembl and Gene Prediction Tools output CDS' not divisible by 3
... Many thanks for the answers. While I guessed it was something like this, I could not find any information in the GFF database providers or ORF prediction tools which state what type of system is being use for any particular file/data. I see it is noted in the link that GFF files are 1-based. Is thi ...
written 6 months ago by NickJD0
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Ensembl and Gene Prediction Tools output CDS' not divisible by 3
... Ensembl and Gene Prediction Tools output CDS' not divisible by 3 I have been looking at a number of different ORF tools such as prodigal and GFF files from databases such as Ensembl and they both report genes/CDS' which are not divisible by 3. Examples below: Chromosome Prodigal_v2.6.2 CDS 686 ...
cds gff orf written 6 months ago by NickJD0 • updated 6 months ago by ATpoint40k

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