I want to draw a dendogram to compare the genomic differences between two bacterial genomes.
Follow bioinformatics tools. PHYLIB program, Multiple sequence analysis, Numerical characterisation of DNA sequences
I recommend you also to use PopGene. After doing your dendrogram in either phylip or PopGene, you can use treeview to visualize the dendrogram in square, radial, or other forms. Other open source programs that can be use to construct dendrogram are TPFGA and Arlequin.
RAPDistance would be better, bur S/W is not user friendly. You must be keen on entering the data.
You can draw a dendrogram with PHYLIP, TFPGA, POPGENE or SPLITS TREE
The RAPD data generally is in the form of bands in agarose gels. hence first convert that into binary score. Once the binary score is achieved, you can enter the score into TREECONW software which is very user friendly for construction of dendrograms using neighbour joining or UPGMA methods.
I am agree with Siva, the RAPD data analysis generally is in the form of bands in agarose gels. hence first convert that into binary score then you can use some of the softwares above mentioned
@Saurabh Dubey,
You have to look at your gel(s), and select one band (fragment/ locus/ allele) at a time, go through all your gels until you evaluate all the individuals: everytime an individ has that band - you put 1 in your data file and 0, if the band is missing (zero allele). Then repeat with the next band and so on untill you evaluate all the bands in all individuals. You may use Excel at the begining, while you are converting gel image into a binary matrix, later you'll just copy that data into a programs required format. Here http://bioinformatics.psb.ugent.be/downloads/psb/Userman/treecon_intro.html
is a nice example 4 (RFLP/AFLP/RAPD data) under Examples of the TREECON format with a binary data consisting only of 1 and 0.
In the given example the same band (fragment) will have the same position in the binary line, so if you go through the matrix verticaly, e.g. fragment no 1 is present in all four individs (samples 1-4) because it has a value of 1, but the second fragment is not present in the 4th individual, so it has a value of 0.
Conversion into binary data can be done manually or by the help of computer packages like https://wheat.pw.usda.gov/jag/papers99/paper599/
I strongly support the explanation given by @Asta Stapulionyte
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