Algorithm 1 Two-level resolution template matching algorithm

Require:  The compressed query sequence $Q_l$ and $Q_h$. Two groups of templates $\left\{T_l\right\}$ and $\left\{T_h\right\}$ with length $N_l$ and $N_h$. The number of templates for each group is denoted as $N_t$.   1:Initial matching scores: $S_l^{max}\leftarrow 0,S_h^{max}\leftarrow 0$.   2:Step 1: Exact matching between $Q_l$ and $\left\{T_l\right\}$:   3:for$i=1$ to $N_t$ do   4:     $S_l^i=1-\frac{d_H(Q_l,T_l^i)}{N_l}$.   5:     if $S_l^i>S_l^{max}$ then   6:         $S_l^{max}\leftarrow S_l^i,C_l^{max}\leftarrow C_i$, where $C_i$ is the ith clade.   7:     end if   8:end for   9:Sort $\left\{S_l^i\right\}$ in descending order: $\left\{S_l^{i^{\prime }}\right\}$. The superscripts $1^{\prime }$ and $2^{\prime }$ are the clade index numbers corresponding to the highest and next highest scores, respectively. 10:if$S_l^{1^{{}^{\prime }}}>S_l^{2^{{}^{\prime }}}$then 11:     $C_l^{*}\leftarrow C_l^{max}$. 12:     return $C_l^{*}$. 13:else 14:     The clade index numbers with the same and the highest score form the set $I_h$, and the size of $I_h$ is $N_t^h$, where $N_t^h\ge 2$. 15:     Continue with Step 2. 16:end if 17:Step 2: Exact matching between $Q_h$ and $\left\{T_h\right\}$: 18:fori in $I_h$ do 19:     $S_h^i=1-\frac{d_H(Q_h,T_h^i)}{N_h}$. 20:     if $S_h^i>S_h^{max}$ then 21:         $S_h^{max}\leftarrow S_h^i,C_h^{max}\leftarrow C_i$, where $C_i$ is the ith clade. 22:     end if 23:end for 24:$C_h^{*}\leftarrow C_h^{max}$. 25:return$C_h^{*}$.