I tried many online tools in order to build a phylogenetic tree from a MSA file consisting of 89 long sequences. Most of the tools gave me an error in the output stating that the file is huge or similar statements. I tried Mobyle at pasteur also, and didnt work too. any suggestions for a good reliable online tool?
Given that the input size limits of on-line services tend to be in the 1 to 10MB region, this suggests that your sequences are very large.
In which case you will likely be better off downloading the appropriate software and performing the tree generation locally. For possible programs see: