The best that I tried in the past was the package "phytools" in R. There is a blog for this package under http://blog.phytools.org/ and a large community so you will find good information via google and many people to ask if there are problems. Please find also this example for the use of phytools for some fish phylogenetics for a specific research: http://rspb.royalsocietypublishing.org/content/281/1789/20141047
Best regards,
Thomas
Try PAUP Phylogenetic Analysis Using Parsimony
PAUP* version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX/VMS, or DOS-based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure. These, along with many other improvements, will make PAUP* 4.0 an even more indispensable tool in comparative biological analysis than were previous editions of the program and manual. PAUP* 4.0 and MacClade 3 use a common data file format (NEXUS), allowing easy interchange of data between the two programs.
Other computer programs in addition to the PAUP are Winclada and TNT, both of which allow for this type of analysis. Both are free. Many times what you have to do is a presence-absence matrix and assign numbers to this and in this way you could build a compelling phylogenetic tree. You can consult well how with the book "Interrelationships of Fishes" by Styassny Parenti and Johnson. If you do not have it I can pass it in pdf. My e-mail address is [email protected]
If you are asking how to construct a phylogenetic tree using fish morphology and meristic characters, then you are not talking about "classical taxonomy".
You have already received several comprehensive and helpful suggestions and advise from four colleagues. You have then been informed about different methods that you may use. However, all of those programs work with a matrix that you will have to build by yourself and this is a most difficult part because, and depending on the list of characters that you have and of their coding, the selected outgroup(s) to polarize characters, and also the composition of the selected ingroup, the results may be different.
Hi. In the case of fish and other animals, If we want to construct a phylogenetic tree, based on morphologic data, we can construct UPGMA tree, and Dendrogram by WARD method for clustering of populations (For each species) by using SPSS and SAS softwares.
Please see this paper:
Sociobiology 64(1): 33-41
DOI: 10.13102/sociobiology.v64i1.1179
Dear Gloria!
What is "classical taxonomy"? If it is not morphology.
With regards.
Dear Aleksey,
You do not have to ask the question to me. Just look what at the beginning of this series of comments. When Raghavan sent the question, below it, it is written Classical taxonomy....
Thus, I am not sure what our colleague wanted to say, so that I quoted it as "classical taxonomy" expecting for some clarification.
Best regards.
Dear Gloria, thanks for your answer.
My understanding is the Classical taxonomy is based on morphological characters. That's why I haven't found contradiction in Raghavan's question.
I am sorry, but evidently I didn't understand of your sentence: "If you are asking how to construct a phylogenetic tree using fish morphology and meristic characters, then you are not talking about "classical taxonomy"."
With regards.
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