These tools make use of specific technologies developed for this site. These technologies may have some advantages and disadvantages over other technologies (see here).
Some requirements to consider while using these tools are:
Local alignment search is actually slower than searches made with BLAST technology. It can take as long as an hour to make a search of a long gene in a single chromosome.
In contrast, it finds alternative matches and these matches in general look more suited for phylogenetic studies given that only full length matches are returned.
Sensitivity level 1 is faster and usually enough unless you are looking for very distant homologs. Sensitivity level one with random selection of chunks is an even faster method and usually enough for not too distant homologs.
The phylogenetic tree generator is actually faster in general than similar softwares, making it possible to generate phylogenetic trees for hundreds of elements in a few minutes or even seconds. Despite that, once the number of elements exceeds one thousand, an exponential effect begins to manifest and the processing time starts growing exponentially. For that reason the number of elements per tree is actually limited to 1500.
The phylogenetic tree generator tool makes use of a bottom up strategy which seems to be well suited for large trees with abundant data. I usually find the trees to make more sense than trees generated with most alternative softwares, but maybe that's only my impression.
Given the limited resources for this project, the number of jobs you can queue is limited and some other parameters, like the length of the sequence, are also limited.
To reduce costs, and given that this project is actually an experiment, the servers processing job queues are only active a few hours per day. You can fill jobs at any time but the jobs will only be attended during the scheduled hours.