Answers.Body: <p>You have to perform an alignment first. Phangorn use phylogenetic estimation and this requires a precise alignment position to track homologous nucleotide mutation. Maximum likelihood theory will assess the probability of a given tree for each homologous nucleotide site, if they are not alignment it can't do it and will violate the assumptions of phylogeny. </p>
  
  <p>If the sequences are different lengths, which it means both nucleotide and indel ('-') sites, it means there hasn't been or there is an error with the alignment. I use <code>muscle</code> these days having previously used <code>clustalo</code>. Its really easy to use and easily configures on a linux server and its super quick. If you get stuck let me know.</p>
  
  <p>I had a look at your alignment and can verify it hasn't been aligned.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-20T07:14:51.947Z
Answers.Text: Once you've run your alignment, you may additionnally think about remove poorly conserved regions, e.g. with Gblocks. It might refine your phylogeny.
Answers.UserDisplayName: thomas duge de bernonville
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-21T09:27:30.767Z
Answers.Text: damn I was using the raw fasta file..got my error I have to use the alignment file
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-19T23:52:48.930Z
Answers.LastActivityDate: 2020-05-19T23:52:48.930Z
Answers.UserDisplayName: M__
Body: <p>Im trying to read a multifasta sequence file into phangorn I get the following error </p>
  
  <pre><code>tipseqfile &lt;- ("abhi_seq/clean_dup_rem.fasta")
  tipseq &lt;- read.phyDat(tipseqfile,format="fasta")
  </code></pre>
  
  <p><a href="https://drive.google.com/open?id=1kTXfnRVjpl3xjZFQUpGaJck9M4d5NSnu" rel="nofollow noreferrer">my file</a></p>
  
  <blockquote>
    <p>Error in read.phyDat(tipseqfile, format = "fasta") : 
          sequences have different length</p>
  </blockquote>
  
  <p>Now is it necessary to have same length of each fasta sequence? or Im doing something wrong </p>
  
Tags: <r><phylogenetics><fasta><phylogeny><phangorn>
Title: phangorn fasta file read error
ThreadText: # phangorn fasta file read error
  
  (Asked by: username_0 on 2020-05-19)
  
  Im trying to read a multifasta sequence file into phangorn I get the following error
  
  ```
  tipseqfile <- ("abhi_seq/clean_dup_rem.fasta")
  tipseq <- read.phyDat(tipseqfile,format="fasta")
  
  ```
  
  [my file](https://drive.google.com/open?id=1kTXfnRVjpl3xjZFQUpGaJck9M4d5NSnu)
  
  > Error in read.phyDat(tipseqfile, format = "fasta") :
  > sequences have different length
  
  Now is it necessary to have same length of each fasta sequence? or Im doing something wrong
  
  **Tags:** r, phylogenetics, fasta, phylogeny, phangorn
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-05-19. Score: 3 | Accepted answer
  
  You have to perform an alignment first. Phangorn use phylogenetic estimation and this requires a precise alignment position to track homologous nucleotide mutation. Maximum likelihood theory will assess the probability of a given tree for each homologous nucleotide site, if they are not alignment it can't do it and will violate the assumptions of phylogeny.
  
  If the sequences are different lengths, which it means both nucleotide and indel ('-') sites, it means there hasn't been or there is an error with the alignment. I use `muscle` these days having previously used `clustalo`. Its really easy to use and easily configures on a linux server and its super quick. If you get stuck let me know.
  
  I had a look at your alignment and can verify it hasn't been aligned.
  
  > **Comments:**
  > **username_2**: Once you've run your alignment, you may additionnally think about remove poorly conserved regions, e.g. with Gblocks. It might refine your phylogeny.  
  > **username_0**: damn I was using the raw fasta file..got my error I have to use the alignment file  
  
  ---
  
  