Alignment
Tree concordance
Missing data
Paper looking at a method to remove non-homologous parts from alignments (working mainly on amino-acid sequences and protein-coding nucleotide sequences).
Paper looking for outlier genes.
Paper using phyparts to map gene tree concordance on the supermatrix tree.
This paper also briefly discusses what cutoff value for support in the input trees to use: they use SH-like support <80 as a cutoff.
Papers looking at the impact of missing data when using ASTRAL and other species-tree estimation methods here and [here]((https://www.ncbi.nlm.nih.gov/pubmed/29029338).
Paper showing that filtering out fragmentary sequences before aligning results in less gene tree estimation errors.