I have the DNA sequence of 20 species, and the data for all characters of these species like (thorax volume, proboscis length, wings and legs length, abdomen length, ........ect), my question is :
1- which kind of file format I should use for interning the sequences in to R?
2- After building the tree How can I connect between the character data that I have and the tree?
R can do just about anything you need for phylogenetics, and then some. However, it cannot perform multiple sequence alignments. I recommend using Geneious (http://www.geneious.com/). It is not free, but it will save you a lot of time. It is well worth the money. In Geneious, you can align sequences, import GenBank sequences, perform various phylogenetic analyses, and manage your sequence data. There is a 30-day free trial. In that time, you could align your sequences and then export them into fasta format for APE.
If you are going to use R, I recommend this book: Analysis of Phylogenetics and Evolution with R, by Emmanuel Paradis. This book will answer your questions. Since you have character data, using R will be good for doing analyses in OUCH and SLOUCH.
Other types of analyes of character and sequence data can be done in R, but another good free package is Mesquite. This has great modules for analyzing discrete data, such as Felsenstein's Independent Contrasts (FIC) and modification of Pagel's DISCRETE method. It is also good for making graphics that trace traits on trees. It is really easy to manipulate trees in Mesquite. For continuous data, I recommend analysis using Pagel's BayesTraits.
http://www.geneious.com/
http://www.springer.com/us/book/9781461417422
http://www.evolution.rdg.ac.uk/BayesTraits.html
http://mesquiteproject.org/
Thank You Allen
can I ask you some question, if it is possible for you through email?
this is my email ( [email protected] )
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