---
name: "trainphd"
section: "1"
platform: "linux"
package: "tracetuner"
version: "3.0.6~beta+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/trainphd"
---

# trainphd(1)

interpretation of DNA Sanger sequencing data

## NAME

trainphd - interpretation of DNA Sanger sequencing data

## DESCRIPTION

- **-h**

  (Help) This message

- **-C** \<consensusfile\>

  Specify the name of the FASTA file which contains the consensus sequence

- **-V** \<vector\>

  Specify the name of the FASTA file which contains the vector sequence

- **-P** \<primer\>

  Specify the name of the FASTA file which contains the primer sequence

- **-S** \<site\>

  Specify the name of the FASTA file which contains the restriction site sequence

- **-M** \<match\>

  Specify the match premium     (default is 10)

- **-X** \<mismatch\>

  Specify the mismatch penalty  (default is 20)

- **-G** \<gap\_penalty \>

  Specify the gap initiation or extension penalty (default is 40)

- **-r** \<repeat\_fraction\>

  Specify the repeat\_fraction   (default is 0.85)

- **-f** \<max\_frac\_of\_err\>

  Specify the allowable fraction of errors within the best alignment region. Default is 0.1. If actual fraction of errors exceeds this vale, the fragment will be rejected (=not used in training process)

- **-a** \<min\_portion\_aligned\> Instructs trainphd to ignore a read if less than

  the specified portion of its bases is aligned with reference sequence (default is 0)

- **-l** \<min\_read\_length\>

  Instructs trainphd to ignore a read of length less than specified number of basepairs (0 by default)

- **-o** \<output\_file\>

  Specify the name of the output file. By default, the output will be made to stdout

- **-t** \<tab\_dir\>

  Instructs trainphd extract alternative base calls from TAB files stored in directory tab\_dir and to output these calls, together with quality value for each alternative call

- **-d** \<dir\>

  Read the input PHD files from specified directory

- **-j** \<projectfile\>

  Specify the name of the projectfile which comprises two columns: the full path to the FASTA file which contains the consensus sequence, followed by the full path to the sample file

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.