The procedures before calculating phylogenetic diversity of a plant community

Question

[shadowstep]

Hi, I'm new to molecular ecology and Biostars. Please don't mind that I have such a stupid question.

For example, I have a plant community with 8 plant species.

I downloaded matK and rbcL sequences for all 8 species from NCBI, respectively, in FASTA format. Therefore I have 2 x 8 sequences.

Now I want to use these files to calculate community phylogenetic diversity, what should I do, to preprocess these files so that they can meet the needs? I've learnt that seqinr, ape and picante can do the job.

I'm a experienced R user, so please point me in a right direction, you don't have to write real code, pseudo-code and package name would be of great help.

Thank you again.

[cschu181]

Make a multiple alignment (ClustalO, MAFFT, MUSCLE, ...), visualize and curate the alignment (remove gap columns, outlier sequences; JalView), use the alignment to calculate a tree (RaxML, PHYLIP), visualise the tree (iTOL).

[shadowstep]

Thanks a lot @cschu181