Below are the answers I received. Many thanks to everyone who kindly wrote me. All the best, Cristina MY QUESTION Dear All, is there some genetic software to measure genetic distance between taxa taking indels into account? We are studying chloroplast DNA in a number of angiosperms, and indels appear to be useful for evolutionary comparisons. Any help and comments will be greatly appreciated. ANSWERS Hi Cristina Please check out my Sys Biol paper via publication link on home page below. I also know that GapCoder may be superceded with IndelCoder in SeqState written by Kai Muller. Müller K 2006. Incorporating information from length-mutational events into phylogenetic analysis. Mol Phyl Evol, 38: 667-676. Müller K 2005. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Appl Bioinformatics, 4: 65-69. These refer to analysis tools, rather than genetic distances, but frame the indel issue well I hope? With best wishes Si Creer Post Doctoral Research Fellow Molecular Ecology and Fisheries Genetics Group School of Biological Sciences University Wales, Bangor Bangor Gwynedd LL57 2UW UK e-mail: s.creer@bangor.ac.uk Tel: +1248 382302 Fax: +1248 371644 Home Page: http://biology.bangor.ac.uk/~bssa0d/ ---------- ciao, tri scrivo in italiano perchè ho visto che sei di ROMA.... puoi usare il software GAPCODER (Young ND, Healy J (2003) GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics, 4, 1-6) che ti permette di ottenere un input file che considera gli indel come presenza-assenza. Qeusto muovo datafile puo poi essere utilizzato in PAUP e in mrbayes 3.1 per calcolare le distanze genetiche. Inoltre, comunque questi due ultimi programmi ti permettono di considerare gli indel come fifth base. Prova ad utilizzare tutti i due i metodi e vedi se ottieni dei risulati diversi. Ciao Federica Costantini Federica Costantini,PhD Laboratorio di Ecologia sperimentale Centro Interdipartimentale di Ricerca per le Scienze Ambientali in Ravenna Università degli Studi di Bologna via S. Alberto, 163 48100 Ravenna tel: +39 0544 937401 fax: +39 0544 937411 e-mail: federica.costantini@unibo.it skype username: fedealpha Pagina WWW: http://www.ecology.unibo.it http://www.ecology.unibo.it/page/federica.htm ----------- Cristina, I've played with coding them as 1 (sequence present) or 0 (sequence absent) or as multi-state characters (where there are several discrete classes of the same indel), and have used AMOVA to analyze sets of indels, both along with and instead of nucleotide sequence differences for the coding sequence. There are cases where they really help, and there are cases where they work better than nucleotide substitutions (typically dominated by transitional changes) for phylogenetic reconstruction. This work is with colleagues who are "just trying things out" and is not yet published, as far as I know. The idea is free. It runs against traditional usage, but the point of the exercise is to figure out the phylogeny, not be politically correct. - Peter Smouse From: SMOUSE@AESOP.Rutgers.edu [ mailto:SMOUSE@AESOP.Rutgers.edu] Sent: Wednesday, March 28, 2007 8:04 AM Subject: other: indels ---------- J. Peter Gogarten gogarten@gmail.com Many programs allow to specify indels as missing data or as a character. Parsimony in Phylip by default uses gaps as a character, PAUP by default has them as missing data. If one treats gaps as characters, larger gaps sometimes are a problem, because each individual position is counted as a character. A solution is treat the individual indel as missing data, and to form additional (0/1) characters for the absence/presence of a gap. --------- Reed A. Cartwright Do you want to include indels in the distance measure or do you want to estimate distance with an algorithm that treats indels as something other than missing data? I can do the latter with my current research project. However, if the former is what you are after, then I caution against it because it would involve nearly arbitrary choices about how to weight indels and indel lengths with respect to substitutions. In my work I use substitutions to establish evolutionary distance and calculate the proportion of indels per substitution. I feel that this is the proper way to do it. Email me if you are interested in my approach. Reed A. Cartwright, PhD http://scit.us/ Postdoctoral Researcher http://www.dererumnatura.us/ Department of Genetics http://www.pandasthumb.org/ Bioinformatics Research Center North Carolina State University Campus Box 7566 Raleigh, NC 27695-7566 Cuiusvis hominis est errare, nullius nisi insipientis in errore perserverare. --Cicero ---------- I have coded indels as unique partitions and code presence or absence as 0 or 1. Jeffrey Lozier PhD Candidate Environmental Science, Policy, and Management University of CA, Berkeley 510-643-6481 jlozier@nature.berkeley.edu http://nature.berkeley.edu/~jlozier ---------- I am happy to introduce a new protein sequence simulator, indel-Seq-Gen: Strope, CL, Scott, SD, and Moriyama, EN. 2007. indel-Seq-Gen: A New Protein Family Simulator Incorporating Domains, Motifs, and Indels. Mol. Biol. Evol. 24(3):640-649. indel-Seq-Gen has the capabilities to simulate heterogeneous evolution, allowing the user to set subsequence parameters, such as amino acid frequencies, differing substitution matrices as well as insertion/deletion parameters such as the length distribution, frequency, and indel model. indel-Seq-Gen also introduces a novel quaternary invariable array that allows unique control of motif conservation. Source code and executable files (Macintosh OSX10.2.8, OSX10.4.7, and Linux) for indel-Seq-Gen is available from: http://bioinfolab.unl.edu/~cstrope/iSG Cory Strope http://bioinfolab.unl.edu/~cstrope Bioinformatics Lab, N169, Beadle Center Cory Strope ---------- Maria Cristina, I have played around some bit with using weighted parsimony to build phylogenetic trees using indels. One has to either estimate a rate of indel formation or arbitrarily assign them a weight, but it is not hard to do. -Jeff Jeffrey Ross-Ibarra email: rossibarra@gmail.com web: rossibarra.googlepages.com Dept. Ecology and Evolutionary Biology University of California Irvine, Ca. 92697 Please tell me what is wrong with Darwinism. I can't see anything wrong with Darwinism. Ernst Mayr ---------- Hi I used to have a couple of references on using indels in phylogenetic analyses. It has been a little while since I thought of it. I will look around to see if I can find them. However, I would be interested in hearing any suggestions or ideas you receive. Thank you sincerely, Chris Christopher M.T. Himes Mammalogy, Burke Museum Department of Biology University of Washington Box 353010 Seattle WA 98195 http://students.washington.edu/himes Dr. Maria Cristina Mosco Universita' di Roma ''La Sapienza'' Dipartimento di Genetica e Biologia Molecolare Via dei Sardi, 70 00185 Roma Tel. 06 4991 7807 - FAX 06 44 41 591 e-mail cristina.mosco@uniroma1.it cristina.mosco@uniroma1.it