I read that the built-in ensemble methods in sklearn use decision trees as basic classifiers. Can I use custom classifiers instead?
If you mean random forest classes, then no, this is currently not possible. The ability to allow other grades was discussed on the scikit-learn mailing list last January, but I don't think any actual code came out of this discussion.
sklearn.ensemble.AdaBoostClassifier, : scikit-learn.org/stable/modules/generated/sklearn.ensemble.AdaBoostClassifier.html base_estimator .
sklearn.ensemble.AdaBoostClassifier
I don't know if this helps, but you can easily compile / combine custom classifiers using the Pipeline utilities: http://scikit-learn.org/stable/tutorial/statistical_inference/putting_together.html#pipelining