Ravichandran Subramaniam,

You should definitely check MUMmer:

- http://mummer.sourceforge.net/

To grab the latest stable release (which is from 2011) kindly check:

- https://sourceforge.net/projects/mummer/files/mummer/3.23/

To grab the latest development release, which is from 2017, kindly check:

- https://github.com/mummer4/mummer/releases

For installation instructions:

- https://github.com/mummer4/mummer/blob/master/INSTALL.md

Hope that helps.

you can prepared its data sets from different sources

after getting the data next step

is to analyze them

These Tools

1. Matlab

2.Python Anaconda

3. R programming and R studio

Thank you for your Suggestion Firas Khalil Khana

I tried Mummer for Alignment but it shows an error "Postnuc Returned Non-Zero"

I Attached the Screenshot

Is there any Idea about the Error?

Ravichandran Subramaniam,

From what I can see in the attached picture, looks like you imported windows formatted files to WSL which confused the sequence parser due to different newline character formats between the two operating systems.

It could also be due to a problem with your Query file having an identical ID with your Reference file.

Here's what I suggest:

1- Use the dos2unix utility on your Query file (the file passed as the second argument) to make the format suitable for the operating system/subsystem you're running it on:

$ dos2unix /mnt/d/Supercentenarian/sP/Ref-chr22.fast

Then attempt to execute the command you were using above.

2- Check the id of the query file (the second argument).

3- While this may be unrelated, but I noticed that the file you're passing as the Query file has 'Ref' in its name. Could it be that you're passing one instead of the other? If so try to switch the files passed as arguments and see if the error disappears.

Hope that helps.

Thankyou Aleksandar S. Sokolovski Firas Khalil Khana

Ravichandran Subramaniam,

Glad I could help.