Dear All,
I have uploaded a new version of DAMBE with the following improvement:
1. Tip-dating based on the least-squares criterion: Some users suggested that the input sequence name format (OTUname@Year) is not sufficient. For example, two viral sequences sampled at the end of 1999 and the beginning of 2000, respectively, could be just a few days apart instead of a whole year apart. I have added two more formats: year with decimals, e.g., OTUname@1999.98 and OTUname[at]DDMMYYYY.
2. Effective number of codons: some users have asked for this function, and it is added with some improvements. In particular, the original formulation handles short sequences poorly and the effective number of codons could be more than 100. I dealt with this problem by adding the option for pseudocount (which I suggest should not be greater than 1, which is also the default). There are also a few other things that I will explain in more detail if you are interested to use the function. The function is accessible by clicking ‘Seq.Analysis|Codon usage|Nc: Effective number of codons’.
3. Numbering notation: After spending a part of my sabbatical in Europe (mostly in Turku, Finland), I have noticed that the European use of ‘,’ for ‘.’ (e.g., 1.234,56 instead of 1,234.56) affects some of DAMBE’s functions. I believe that I have fixed them all. Please let me know if you experience anything unusual.
Please download the new version.
For those who do not know DAMBE, it is a comprehensive software package for extensive data analysis in molecular biology and evolution for Windows ME/2000/XP/VISTA but can be run on Intel-based Mac and Linux systems with WINE. It is freely available at
http://dambe.bio.uottawa.ca/dambe.asp
You can find publications that used DAMBE by using Google scholar at:
http://scholar.google.com/scholar?as_q=3Dnum=3D100btnG=3DSearch+Scholaras_epq=as_oq=as_eq=as_occt=anyas_sauthors=Xuhua+Xiaas_publication=as_ylo=as_yhi=as_sdt=1.as_sdtp=onas_sdtf=as_sdts=5hl=en
Xuhua Xia
Professor, Bioinformatics and Molecular Evolution
Biology Department
University of Ottawa
Rm 278 Gendron
30 Marie Curie, Ottawa, Ontario Canada K1N 6N5
Tel: (613) 562-5800 ext 6886
URL: http://dambe.bio.uottawa.ca