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Today, I will talk to you about how to carry out one-click Batch Compute ka and ks. Many people may not know much about it. In order to let you know more, Xiaobian summarizes the following contents for you. I hope you can gain something according to this article.

ParaAT installation

1. Download ParaAT 2.0

（https://bigd.big.ac.cn/tools/paraat）

After decompression,"ParaAT.pl" is the script that runs. You can add the unzipped path to an environment variable, or you can run the script at the absolute path.

2. Install the required dependency tools, dependency tools need to add environment variables

Protein comparison tool, recommended installation of muscle, the effect of comparison is relatively best, faster than, but

It consumes more memory than other tools.

KaKs_Calculator (http://bigd.big.ac.cn/tools/kaks)

Prepare input file

1. List of homologous genes, file format:

geneA1 geneA2 geneA3geneB1 geneB2 geneB3geneC1 geneC2 geneC3geneD1 geneD2 geneD3

Each row represents a group of homologous genes, and each column represents the corresponding gene for each species. The gene IDs are separated by tabs.

2. fasta format protein sequence file and nucleic acid sequence file, note that gene ID should be consistent with ID in homologous gene list file;

3. A file that runs multithreaded, specifying the number of threads.

This file only needs to write a number indicating how many threads are running simultaneously.

Three sample files can be found in the extracted installation package: test.homologs, test.pep, test.cds, proc

Run ParaAT

The code is as follows:

ParaAT.pl -h test.homologs -n test.cds -a test.pep -p proc -m muscle -g -k -o result_dir

-h, specifies the homologous gene list file

-n, specifies the nucleic acid sequence file

-a, specifies the protein sequence file

-p, specifies multithreaded files

-m, specify matching tool

-g, remove the gap codon

-k, calculate kaks value with KaKs_Calculator

-o, output directory of results

Note:

1. If you need to analyze kaks with PAML, Hyphy, etc., ParaAT can also generate the input files required by these tools (-f parameter)

2. If it is a bacterial sequence, it needs to be set to the corresponding Genetic Code used (-c 11) of the bacteria. The default is The Standard Code (-c 1).

After reading the above, do you have any further understanding of how to perform one-click Batch Compute ka and ks? If you still want to know more knowledge or related content, please pay attention to the industry information channel, thank you for your support.

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