the main server is usually working at
[1] if it is down try [2]

Phylogeny is changing with the number of sequences

This is not a real problem and fairly normal, but it is rather confusing.
The best way to do is to begin with a low number of sequences to align (30) and if necessary (the tree has no external root outside the closest species of the query) increase gradually. Be aware, more time is needed for computing !
The is an optimal number of sequences for each problem, depending of both the query (its species) and the database.

Phylogeny is changing with the gaps options

There are two options to construct the tree, each option give a different tree :

Not exclude positions with gaps (default)
- better phylogeny as all the information is used
Exclude positions with gaps
- only the common positions existing in the sequences are used, so the phylogeny is less discriminative, but computing is easier.

Undetermined Bug during computing

The label :

http://umr5558-mq1.univ-lyon1.fr/WIKIS/mq_wiki/attachments/bibiW2.png

indicate that a bug occurs. This is fairly rare now. This is mainly due to computing problems during the construction of the HTML tree, and the tree may be only partially computed.

open the "The FILES for further work by your own" directory and and have a look to rootedset.txt
send a mail to flandrs at biomserv dot univ-lyon1 dot fr with your sequence
most of the cases are due to typographical problems in the sequence identification (a remaining "," or "(" for instance).

No BLAST hits

The following information is given :

http://umr5558-mq1.univ-lyon1.fr/WIKIS/mq_wiki/attachments/bibiW6.png

Check the database, may be you selected a wrong one.
Check the sequence, copy-paste actions are sometimes confusing and the Fasta Format must be correct

Small DNA segment

Here is the information :

http://umr5558-mq1.univ-lyon1.fr/WIKIS/mq_wiki/attachments/bibiW1.png

Check the database, may be you selected a wrong one.

No Real Tree

http://umr5558-mq1.univ-lyon1.fr/WIKIS/mq_wiki/attachments/bibiW3.png

This may be due to biological reasons :
- the sequences are identical or very closely related AND the number of these sequences is bigger than the number of sequences you have choosen in the first step
  - increase the number of recruited sequences in the first step of Bibi Le
  - if you are using SSUrDNA (16S), try the TS database containing only TS and complete genomes.
- the sequences are very divergent, so alignment problems occurs
  - look at the alignment
- the tree cannot be computed correctly
  - change the toss gap option (choose 'exclude positions with gaps' instead of 'Not exclude positions with gaps'

Lack of biodiversity

In the case of :

http://umr5558-mq1.univ-lyon1.fr/WIKIS/mq_wiki/attachments/bibiW5.png

This is due to biological reasons :
- the sequences are identical or very closely related AND the number of these sequences is bigger than the number of sequences you have choosen in the first step
  - increase the number of recruited sequences in the first step of Bibi Le
  - if you are using SSUrDNA (16S), try the TS database containing only TS and complete genomes.