1. Folder 'CAEC_haplo' includes code for haplotype assembly. More details can be found in Readme.txt file in folder 'CAEC_haplo'.

2. Folder 'CAEC_viral' includes code for viral quasispecies reconstruction. More details can be found in Readme.txt file in folder 'CAEC_viral'.

3. Folder 'HIV-1' includes HIV-1 data, pretrained models of CAECseq and code for evaluation. More details about using pretrained models to evaluate the performance of CAECseq on HIV-1 data can be found in Readme.txt file in folder 'HIV-1'.

4. Folder 'Solanum_Tuberosum_Semi_Experimental' includes semi-experimental 'Solanum Tuberosum data with sequencing coverage 5, 15 and 25.

5. Due to the limitation of the size of supplementary material, data used in both the main paper and supplementary document can be downloaded at (https://drive.google.com/file/d/1PQJrvMPWvBZ3SIef0R1ESED7huk1ikgr/view?usp=sharing).