User: Fid_o
Fid_o • 20
- Reputation:
- 20
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- New User
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- Last seen:
- 5 months, 3 weeks ago
- Joined:
- 1 year, 6 months ago
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I am a Bioinformatics student, quite new in the field.
Posts by Fid_o
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... Greetings,
Is there a way to extract evolutionary lineages from phylogenetic trees? I am working on 465 bacterial sequences. The bacteria I am working with has known Lineage 1 and Lineage 2. I am examining the emergence of a newer lineage, which I will call 2.1. I do not know how many of the seque ...
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... Thank you for that help and insight. Absolutely helpful. ...
written 6 months ago by
Fid_o • 20
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... @genomax. Thank you for your replies. I needed quality check for my SNP analysis on these sequences. ...
written 6 months ago by
Fid_o • 20
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... @genomax I don't have the fasta/qual files, it's just the fasta files.
This being the case, can I safely convert fasta files to fastq for purpose of FASTQC use? My first reservations with conversion would be possibility of introducing errors to the files. ...
written 6 months ago by
Fid_o • 20
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... @genomax, I mean to check the quality like we would check using FASTQC. I realise FASTQC takes in Fastq files, I have .FASTA files. ...
written 6 months ago by
Fid_o • 20
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... Hello,
I have .FASTA files of bacterial genomes. I want to check quality of the sequences. Which program accepts quality analysis of .FASTA files?
Cheers! ...
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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 7 months ago by
Fid_o • 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 7 months ago by
Fid_o • 20
• updated
7 months ago by
Mensur Dlakic • 6.9k
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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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