User: Fido
Fido • 20
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- 11 months, 3 weeks ago
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I am a Bioinformatics student, quite new in the field.
Posts by Fido
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... I would like to generate a Neighbour Joining (NJ) tree from a FASTA alignment I have (from bacterial sequences). What better software is available for this? ...
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... Greetings,
I have a group of sequences from bacterial genome which I want to separate into lineage-sublineage. I have reference genome for the parent lineage and a reference genome for the sublineage. These are separated by differences in SNPs. What good software or code would I use to pull out th ...
written 24 days ago by
Fido • 20
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... I ran roary on sequences and I have an aligned file with the extension .aln. I would like to run this aligned file on RAxML which needs a .phy file. How do I convert .aln file to sequential .phy? ...
written 28 days ago by
Fido • 20
• updated
28 days ago by
Mensur Dlakic • 4.3k
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... I run roary ( roary -e --mafft -p 32 *.gff) to produce core genome alignment on hundreds of Salmonella sequences and have results. I have the following files in the results:
1. gene_presence_absence.csv
2. gene_presence_absence.Rtab
3. pan_genome_reference.fa
4. accessory_binary_genes.fa.newick
5 ...
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... Thank you sooooo much Mensur Dlakic.
I am learning Bioinformatics and your help is great. ...
written 4 weeks ago by
Fido • 20
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... I ran this annotation command: for k in *.fasta; do prokka $k --outdir "$k".prokka.output; echo $k; done
on hundreds of assembled sequences. Each sequence annotation output produced a folder named "sequence_name.prokka.output" but the actual files in the folders were named according to the date e ...
written 4 weeks ago by
Fido • 20
• updated
4 weeks ago by
Mensur Dlakic • 4.3k
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... Greetings @ATpoint!
Thanks for that reply.
I want to do core and accessory gene analysis using roary. I will later be doing phylogenetics. I want to remove all sequences that are too small or too large as, from what I was told, a too small size would mean only a shorter part of the genome was sequ ...
written 4 weeks ago by
Fido • 20
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... I have whole genome sequence data (.FASTA files) for Salmonella bacteria. On average the sequence files have a size of 4.7MB but there are some that are too big, like 7Mb and others that are too small, like 500Kb. There is likelihood that the too large files contain unnecessary sequence data and the ...
written 4 weeks ago by
Fido • 20
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... I have 900 assembled Salmonella Typhimurium ST313 sequences (.FASTA files, average sequence size 4.7MB). Basic information says there are two lineages of salmonella strains - one an old lineage and another a newer one. The newer one has 22 SNP differences from the old one.
I need to separate which ...
written 4 weeks ago by
Fido • 20
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... I have over 900 assembled genomes which I want to annotate using prokka. Previously I have annotated few sequences by running each one by one, but with 900 I need a python script to automate the process.
Can anyone share a script that can be adopted to do my annotation, please.
Regards. ...
written 3 months ago by
Fido • 20
• updated
3 months ago by
Mensur Dlakic • 4.3k
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