Chengze Shen

TIPP-SD improves species detection accuracy in microbiomes, especially for low-abundance species and with sequencing errors, while maintaining reasonable speed.

TIPP3 and TIPP3-fast improve metagenomic abundance profiling accuracy, especially for novel genomes and error-containing reads, with TIPP3-fast offering faster runtime while maintaining high accuracy.

EMMA adds unaligned sequences to a constraint alignment with high accuracy and scalability for large datasets.

BATCH-SCAMPP improves phylogenetic placement scalability by enabling efficient batch processing of query sequences on large trees.

SALMA improves multiple sequence alignment accuracy and scalability for large datasets with high evolutionary rates and sequence length variation.

UPP2 improves alignment accuracy for large datasets with sequence length heterogeneity by reducing runtime while maintaining accuracy comparable to UPP.