Answers.Body: <p>Thanks the qstart and stop are not needed. If you using 'blockwise deletion' in your phylogenetic tree it will ignore the missing sites if this options is selected.</p>
  <p>The main thing is <code>CAKANA010000013.1</code>   and <code>215358.XP_010753781.1</code></p>
  <p>215358 this is the species identification and XP_010753781.1 is the NCBI code for the gene. Thus if you now blast your top this like so,</p>
  <p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&amp;PROGRAM=blastp&amp;DATABASE=nr&amp;LINK_LOC=gquery&amp;QUERY=XP_010753781.1" rel="nofollow noreferrer">https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&amp;PROGRAM=blastp&amp;DATABASE=nr&amp;LINK_LOC=gquery&amp;QUERY=XP_010753781.1</a></p>
  <p>This will generate a range of homologous genes that you will require as supporting data for your tree.</p>
  <p>The gene is zonadhesin isoform X1 and species <em>Larimichthys crocea</em></p>
  <p><code>CAKANA010000013.1</code> should be the internal nomenclature for the underlying eggNOG alignment, but I am having trouble finding it from the eggNOG database at present. However, it should be there somewhere.</p>
  
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Body: <p>I used Eggnog mapper to annotate several rockfish genomes and the output files have qstart and qend values for each gene.</p>
  <p>I plan to use the phylogenetic trees for a few different genes for positive selection analyses using HyPhy. The data is whole scaffold level rockfish genomes pulled from NCBI. The output files from eggnog have something like 20000 genes but I only plan to use a few of those.</p>
  <p>The first few lines of the eggnog output look like this:</p>
  <pre><code>##/home/user/anaconda3/envs/3.8env/bin/diamond blastx -d '/home/totorbanana/anaconda3/envs/3.8env/lib/python3.8/site-packages/data/eggnog_proteins.dmnd' -q '/home/totorbanana/Genomes/Mystinus.fna' --threads 1 -o '/home/user/Genomes/test.emapper.hits' --tmpdir '/home/user/Genomes/emappertmp_dmdn_ltcz8hno' --sensitive --iterate -e 0.001 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp
  #qseqid sseqid  evalue  bitscore    qstart  qend    sstart  send    pident  qcov    scov
  CAKANA010000013.1   215358.XP_010753781.1   1.14e-27    123.0   1020    844 1708    1766    89.8    16.0    2.1
  CAKANA010000020.1   215358.XP_010753832.1   4.68e-292   854.0   1410    3083    1   558 79.8    31.0    100.0
  </code></pre>
  <p>What I am unsure of is how to use those qstart and qend values to extract the corresponding sequences and make a multiple sequence alignment with them.</p>
  <p>If anybody could offer guidance/advice I would be very appreciative.</p>
  
Tags: <phylogenetics><genome>
Title: Creating a Multiple Sequence Alignment From Eggnog Mapper Results
ThreadText: # Creating a Multiple Sequence Alignment From Eggnog Mapper Results
  
  (Asked by: username_0 on 2024-05-20)
  
  I used Eggnog mapper to annotate several rockfish genomes and the output files have qstart and qend values for each gene.
  
  I plan to use the phylogenetic trees for a few different genes for positive selection analyses using HyPhy. The data is whole scaffold level rockfish genomes pulled from NCBI. The output files from eggnog have something like 20000 genes but I only plan to use a few of those.
  
  The first few lines of the eggnog output look like this:
  
  ```
  ##/home/user/anaconda3/envs/3.8env/bin/diamond blastx -d '/home/totorbanana/anaconda3/envs/3.8env/lib/python3.8/site-packages/data/eggnog_proteins.dmnd' -q '/home/totorbanana/Genomes/Mystinus.fna' --threads 1 -o '/home/user/Genomes/test.emapper.hits' --tmpdir '/home/user/Genomes/emappertmp_dmdn_ltcz8hno' --sensitive --iterate -e 0.001 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp
  #qseqid sseqid  evalue  bitscore    qstart  qend    sstart  send    pident  qcov    scov
  CAKANA010000013.1   215358.XP_010753781.1   1.14e-27    123.0   1020    844 1708    1766    89.8    16.0    2.1
  CAKANA010000020.1   215358.XP_010753832.1   4.68e-292   854.0   1410    3083    1   558 79.8    31.0    100.0
  
  ```
  
  What I am unsure of is how to use those qstart and qend values to extract the corresponding sequences and make a multiple sequence alignment with them.
  
  If anybody could offer guidance/advice I would be very appreciative.
  
  **Tags:** phylogenetics, genome
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-05-21. Score: 1 | Accepted answer
  
  Thanks the qstart and stop are not needed. If you using 'blockwise deletion' in your phylogenetic tree it will ignore the missing sites if this options is selected.
  
  The main thing is `CAKANA010000013.1` and `215358.XP_010753781.1`
  
  215358 this is the species identification and XP\_010753781.1 is the NCBI code for the gene. Thus if you now blast your top this like so,
  
  <https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROGRAM=blastp&DATABASE=nr&LINK_LOC=gquery&QUERY=XP_010753781.1>
  
  This will generate a range of homologous genes that you will require as supporting data for your tree.
  
  The gene is zonadhesin isoform X1 and species *Larimichthys crocea*
  
  `CAKANA010000013.1` should be the internal nomenclature for the underlying eggNOG alignment, but I am having trouble finding it from the eggNOG database at present. However, it should be there somewhere.
  
  > **Comments:**
  > **username_0**: Thank you for the help!  
  
  ---
  
  