Genemapper

[ronf]

Hello! I am working for the first time with AFLP . I cannot export the table from genemapper as it has too much columns. Is that normal? Is there any tool to rearrange this? I have up to 400 loci and 280 samples. How do I prepare an input for population genetic software like Phylip?

Thank you!

[ani1977]

Originally Posted by ronf

Hello! I am working for the first time with AFLP . I cannot export the table from genemapper as it has too much columns. Is that normal? Is there any tool to rearrange this? I have up to 400 loci and 280 samples. How do I prepare an input for population genetic software like Phylip?

Thank you!

Check out PERL ActiveState and tutorial Essential Perl to get going.
All the best,
Animesh

[ronf]

Thank you Animesh! I´ll take a look. In the meanwhyle my husband wrote a script with R and it works. But he had also adviced me, I won´t come out of this analysis without learning to programm. So I will try to learn PERL.

By the way, I was visiting some weeks ago the links you posted in the BioTechniques forum, they are really good and it is nice to see how much enthusiams you have in your research. I wish you much success!

Have a nice sunday and thank you again for your advice,

ron.

[ani1977]

Originally Posted by ronf

Thank you Animesh! I´ll take a look. In the meanwhyle my husband wrote a script with R and it works. But he had also adviced me, I won´t come out of this analysis without learning to programm. So I will try to learn PERL.

By the way, I was visiting some weeks ago the links you posted in the BioTechniques forum, they are really good and it is nice to see how much enthusiams you have in your research. I wish you much success!

Have a nice sunday and thank you again for your advice,

ron.

Hey Ron,
Yes R is very good for your purpose.
Without picking up a programming language, it will not be fun to do such stuff. PERL is easy and popular with loads of support, so get going. There is perl-r bridge [ RSPERL: www_omegahat_org/download/R/packages/RSPerl.tar.gz ] which helps in calling R via PERL and vice-versa.
Thanks for the good wishes, I need a lot of it
Regards,
Animesh

[ronf]

Hallo Animesh!
That´s a great tip! I am really amazed about how many things I am discovering in the world of "genetics-programming". And I have still so much to learn! I am really thankful to those of you who already made a part of the way in programming and that can help me now.

Kind regards,

Ron

Originally Posted by ani1977

Hey Ron,
Yes R is very good for your purpose.
Without picking up a programming language, it will not be fun to do such stuff. PERL is easy and popular with loads of support, so get going. There is perl-r bridge [ RSPERL: www_omegahat_org/download/R/packages/RSPerl.tar.gz ] which helps in calling R via PERL and vice-versa.
Thanks for the good wishes, I need a lot of it
Regards,
Animesh

[ani1977]

Hey Ron,
Glad to hear that you are enjoying your journey Since you are beginning, I would also recommend to pick up JAVA and BioMOBY specifically. I have compiled some links and directions on how to go about this at computationalbiologynews_blogspot_com/2007/06/promex_html [ replace _ with . ].
Btw you can call this bioinformatics but not "genetics-programming" because genetic-programming is a machine learning field where we manipulate the operators between the interacting variables. It is a very interesting field where computer program try to simulate evolution in the some-what biological sense. More details on en_wikipedia_org/wiki/Genetic_programming [ replace _ with . ].
Enjoy,
Ani

Originally Posted by ronf

Hallo Animesh!
That´s a great tip! I am really amazed about how many things I am discovering in the world of "genetics-programming". And I have still so much to learn! I am really thankful to those of you who already made a part of the way in programming and that can help me now.

Kind regards,

Ron

[ronf]

I had no idea, that "genetics-programming" a research field itsself is. By the way, great blog, I sended it also to my colleges. Have a nice sommer!

Ron

[ani1977]

Hey Ron, thanks again for appreciating the blog and spreading it amongst your friends
It is raining here in Delhi (India), monsoon time. Are you German?
Regards,
Ani

Originally Posted by ronf

I had no idea, that "genetics-programming" a research field itsself is. By the way, great blog, I sended it also to my colleges. Have a nice sommer!

Ron

[ronf]

Originally Posted by ani1977

Hey Ron, thanks again for appreciating the blog and spreading it amongst your friends
It is raining here in Delhi (India), monsoon time. Are you German?
Regards,
Ani

I sent it to my "ex-labmates" in Spain. I´m not german, I come from Spain but I´m living in Germany since 7 years. My husband is german. And my grandfather was it too! so I like the country very much :-)

Hiere it has been raining the whole time, but I guess, not so much as the monsoon rains! and since two days it is very hot and humid.

I send you a web site that I consider very useful to write papers. You may already know it: www_wordindex_org

Have a nice monsoon time!

Ron