It is not surprising becayse you analyse very close taxa. For secondary structure reconstruction you are ble to use standard metods and services. Structures are very conservative an stable in most of cases. This may help you to see that different parts have different conservacy and informativity. As an example, if you detect hCBC or CBC you can conclude that you have two differet taxa etc.

There are some tools and literature references about this:

its2.bioapps.biozentrum.uni-wuerzburg.de

http://mfold.rna.albany.edu/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370725/

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066726

http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000001181/03_kap3.pdf;jsessionid=B69F2CFFBEACB89F3DF3F077D233AA62?hosts=

low P-value only can show data sitribution. If you mean this problem, you can enchanced this situation by increasing of number of sequences in sampling. If you mean less of bustrap value, this may be caused by some reasons:

1. sequences are very similar with very small quantity of base changes

2. sequences are very short

3. you analyse only a few similar sequences

You can minimize some of these problems by increasing of number of sequences in sampling, increasing lenth of sequences.

In case if you have primary sequence data, you must check your sequence chromatogram to detect full equivalence between peaks and letters . But nothing more corrections you can't be able to do

I want to construct a phylogenetic tree with 10 sequence data, among which 4 are from the same species collected by me from different localities in different years. Remaining 4 are from closely related species of the species I collected and two are the outgrouping taxa. The problem of low bootstrap support arise when I am going to construct MP tree in MrBayes. But insterestingly when I am constructing tree with MEGA4 in NJ method the tree is getting enough bootstrap support. All of the sequences I have is approximately 650 bp (ITS1-5.8s-ITS2) So, there might not be any problem with very short sequence length. Now what should I do!!

I have similar problems in ITS1-5.8S-ITS2 phylogeny costruction. NJ is distant method and its algorhytm greatly differ from MP. Try to use also ML and other methods and construct consensus tree. Also I recommend to increase sequeces number from NCBI or similar resorces to see the result. Another principally different method, but good for ITS based phygeny reconstruction is recostruction of its secondary structure/ In such way you can estimate differences between specimens more precisely.

How would I reconstruct ITS based phylogeny by reconstructing its secondary structure to estimate differences?

My collected species is a new species and I have got that species from different regions of my Country in different years. I have four sequence of (ITS1-5.8s-ITS2; 650 bp) as well as partial LSU (670 bp) of that species. Most of the journals accept MP trees, so I should incorporate MP trees; I surprised when I am getting low PP support in both the cases (ITS and nLSU rDNA).

It is not surprising becayse you analyse very close taxa. For secondary structure reconstruction you are ble to use standard metods and services. Structures are very conservative an stable in most of cases. This may help you to see that different parts have different conservacy and informativity. As an example, if you detect hCBC or CBC you can conclude that you have two differet taxa etc.

There are some tools and literature references about this:

its2.bioapps.biozentrum.uni-wuerzburg.de

http://mfold.rna.albany.edu/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370725/

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066726

http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000001181/03_kap3.pdf;jsessionid=B69F2CFFBEACB89F3DF3F077D233AA62?hosts=

Thanks to all......I have solve the problems....

Thank u all once again......................