how to increase accurancy of phylogenetic tree

[hianghao]

I've constructed a tree based on my interest genes using NJ method, 10000 bootstrap. Some of the branches showed low confidence level, ie 30 stg to 60 stg. How can i improve it? Or it would be fine like that? What are the probable explanation for this?

[landscape031]

I am also interested in this question, hope somebody can do a help!!!

[fiedel]

Improving the Accuracy of Phylogenetic Estimation by Combining Different Methods

Three methods of phylogenetic tree estimation, UPGMA clustering (UP), maximum parsimony (MP), and neighbor joining (NJ), were used to estimate trees from a large simulation study of 5,400 eight-taxon data sets. The data sets represented nine evolutionary models and 20 tree topologies. The agreement of the trees estimated by the three methods was highly correlated (0.71) with the average agreement with the true tree from which the data sets had been generated. A simple index is proposed for the agreement of different estimation methods that can serve as a measure of the reliability of the joint estimate. This index was coupled with an unbiased character weighting procedure to increase the accuracy of estimation. Accuracy was increased by an average of 24% by use of this procedure in 47 of 61 data sets examined.

[JanChang]

Got a relevant but silly question here. While doing multiple alignment and constructing a tree, do people trim all the compared sequences to the same length? For instance, say I have five sequences for comparison as shown below.

#1 ------------------------------------------------------------------
#2 -----------------------------------------------------------------------------------
#3 ------------------------------------
#4 -----------------------------------------------------------
#5 -------------------------------------------------------------------------------------

Is it necessary to trim them to preserve only the overlapped region, such as
## ------------------------------------
, or just leave it as they are, or any other ways people are used to doing by convention? Thank you very much.

[richardshelton]

The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.