User: Fid_o

gravatar for Fid_o
Fid_o20
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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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s***********@gmail.com

I am a Bioinformatics student, quite new in the field.

Posts by Fid_o

<prev • 21 results • page 1 of 3 • next >
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Extracting lineages from phylogenetic trees
... 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 ...
lineage phylogenetics alignment written 6 months ago by Fid_o20 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: Quality check of sequences in fasta format
... Thank you for that help and insight. Absolutely helpful. ...
written 6 months ago by Fid_o20
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Comment: C: Quality check of sequences in fasta format
... @genomax. Thank you for your replies. I needed quality check for my SNP analysis on these sequences. ...
written 6 months ago by Fid_o20
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Comment: C: Quality check of sequences in fasta format
... @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_o20
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Comment: C: Quality check of sequences in fasta format
... @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_o20
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Quality check of sequences in fasta format
... 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! ...
genome assembly alignment written 6 months ago by Fid_o20 • updated 6 months ago by genomax91k
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Generating Neighbour Joining Tree from Sequences
... 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? ...
genome sequence snp written 7 months ago by Fid_o20 • updated 7 months ago by lagartija90
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Lineage Separation of Bacterial Sequences
... 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 ...
gene alignment sequence snp written 7 months ago by Fid_o20
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CONVERT .aln file to .phy for RAxML input
... 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? ...
alignment written 7 months ago by Fid_o20 • updated 7 months ago by Mensur Dlakic6.9k
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Visualising Roary Results
... 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 ...
genome sequence alignment roary snp written 7 months ago by Fid_o20 • updated 8 days ago by herber40

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